Gene Name Error Monthly Dashboard
Mark Ziemann
2021-06-08
Source: https://github.com/markziemann/GeneNameErrors2020
View the reports: http://ziemann-lab.net/public/gene_name_errors/
Intro
Gene name errors result when data are imported improperly into MS Excel and other spreadsheet programs (Zeeberg et al, 2004). Certain gene names like MARCH3, SEPT2 and DEC1 are converted into date format. These errors are surprisingly common in supplementary data files in the field of genomics (Ziemann et al, 2016). This could be considered a small error because it only affects a small number of genes, however it is symptomtic of poor data processing methods. The purpose of this script is to identify gene name errors present in supplementary files of PubMed Central articles in the previous month.
library("jsonlite")
library("xml2")
library("reutils")
library("readxl")Get PMC IDs
Here I will be getting PubMed Central IDs for the previous month.
Start with figuring out the date to search PubMed Central.
DATE="2021/4"Let’s see how many PMC IDs we have in the past month.
QUERY ='((genom*[Abstract]))'
ESEARCH_RES <- esearch(term=QUERY, db = "pmc", rettype = "uilist", retmode = "xml", retstart = 0,
retmax = 5000000, usehistory = TRUE, webenv = NULL, querykey = NULL, sort = NULL, field = NULL,
datetype = NULL, reldate = NULL, mindate = DATE, maxdate = DATE)
pmc <- efetch(ESEARCH_RES,retmode="text",rettype="uilist",outfile="pmcids.txt")## Retrieving UIDs 1 to 500## Retrieving UIDs 501 to 1000## Retrieving UIDs 1001 to 1500## Retrieving UIDs 1501 to 2000## Retrieving UIDs 2001 to 2500## Retrieving UIDs 2501 to 3000## Retrieving UIDs 3001 to 3500pmc <- read.table(pmc)
pmc <- paste("PMC",pmc$V1,sep="")
NUM_ARTICLES=length(pmc)
NUM_ARTICLES## [1] 3246writeLines(pmc,con="pmc.txt")Run the screen
Now run the bash script. Note that false positives can occur (~1.5%) and these results have not been verified by a human.
Here are some definitions:
NUM_XLS = Number of supplementary Excel files in this set of PMC articles.
NUM_XLS_ARTICLES = Number of articles matching the PubMed Central search which have supplementary Excel files.
GENELISTS = The gene lists found in the Excel files. Each Excel file is counted once even it has multiple gene lists.
NUM_GENELISTS = The number of Excel files with gene lists.
NUM_GENELIST_ARTICLES = The number of PMC articles with supplementary Excel gene lists.
ERROR_GENELISTS = Files suspected to contain gene name errors. The dates and five-digit numbers indicate transmogrified gene names.
NUM_ERROR_GENELISTS = Number of Excel gene lists with errors.
NUM_ERROR_GENELIST_ARTICLES = Number of articles with supplementary Excel gene name errors.
ERROR_PROPORTION = This is the proportion of articles with Excel gene lists that have errors.
system("./gene_names.sh pmc.txt")
results <- readLines("results.txt")
XLS <- results[grep("XLS",results,ignore.case=TRUE)]
NUM_XLS = length(XLS)
NUM_XLS## [1] 4276NUM_XLS_ARTICLES = length(unique(sapply(strsplit(XLS," "),"[[",1)))
NUM_XLS_ARTICLES## [1] 686GENELISTS <- XLS[lapply(strsplit(XLS," "),length)>2]
#GENELISTS
NUM_GENELISTS <- length(unique(sapply(strsplit(GENELISTS," "),"[[",2)))
NUM_GENELISTS## [1] 496NUM_GENELIST_ARTICLES <- length(unique(sapply(strsplit(GENELISTS," "),"[[",1)))
NUM_GENELIST_ARTICLES## [1] 231ERROR_GENELISTS <- XLS[lapply(strsplit(XLS," "),length)>3]
#ERROR_GENELISTS
NUM_ERROR_GENELISTS = length(ERROR_GENELISTS)
NUM_ERROR_GENELISTS## [1] 228GENELIST_ERROR_ARTICLES <- unique(sapply(strsplit(ERROR_GENELISTS," "),"[[",1))
GENELIST_ERROR_ARTICLES## [1] "PMC8082928" "PMC8082814" "PMC8082497" "PMC8079172" "PMC8072132"
## [6] "PMC8079977" "PMC8078050" "PMC8054196" "PMC8072452" "PMC8072156"
## [11] "PMC8071957" "PMC8064208" "PMC8062533" "PMC8060030" "PMC8056605"
## [16] "PMC8052759" "PMC8052083" "PMC8050920" "PMC8051109" "PMC8048365"
## [21] "PMC8048084" "PMC8048360" "PMC8048283" "PMC8042104" "PMC8034727"
## [26] "PMC8031408" "PMC8024315" "PMC8022387" "PMC8025811" "PMC8046355"
## [31] "PMC8017017" "PMC8016308" "PMC8045971" "PMC8044451" "PMC8027763"
## [36] "PMC8012360" "PMC8011181" "PMC8043114" "PMC8042384" "PMC8009959"
## [41] "PMC8033158" "PMC8020666" "PMC7997954" "PMC7994904" "PMC8025671"
## [46] "PMC7990179" "PMC7985503" "PMC7985195" "PMC8059334" "PMC8011804"
## [51] "PMC7979861" "PMC7979819" "PMC8012900" "PMC7971549" "PMC7993683"
## [56] "PMC8027276" "PMC8050775" "PMC8031731" "PMC8061397" "PMC8017720"
## [61] "PMC7790035" "PMC8054830" "PMC7507402" "PMC7521923" "PMC7993145"
## [66] "PMC7567904" "PMC7610570" "PMC8027439" "PMC8019017" "PMC7608103"
## [71] "PMC7609296" "PMC7608117"NUM_ERROR_GENELIST_ARTICLES <- length(GENELIST_ERROR_ARTICLES)
NUM_ERROR_GENELIST_ARTICLES## [1] 72ERROR_PROPORTION = NUM_ERROR_GENELIST_ARTICLES / NUM_GENELIST_ARTICLES
ERROR_PROPORTION## [1] 0.3116883Look at the errors detected
Here you can have a look at all the gene lists detected in the past month, as well as those with errors. The dates are obvious errors, these are commonly dates in September, March, December and October. The five-digit numbers represent dates as they are encoded in the Excel internal format. The five digit number is the number of days since 1900. If you were to take these numbers and put them into Excel and format the cells as dates, then these will also mostly map to dates in September, March, December and October.
#GENELISTS
ERROR_GENELISTS## [1] "PMC8082928 /pmc/articles/PMC8082928/bin/13073_2021_883_MOESM2_ESM.xlsx Hsapiens 1 43896"
## [2] "PMC8082814 /pmc/articles/PMC8082814/bin/13059_2021_2334_MOESM1_ESM.xlsx Hsapiens 2 44086 44083"
## [3] "PMC8082814 /pmc/articles/PMC8082814/bin/13059_2021_2334_MOESM1_ESM.xlsx Hsapiens 1 44089"
## [4] "PMC8082814 /pmc/articles/PMC8082814/bin/13059_2021_2334_MOESM3_ESM.xlsx Hsapiens 32 44262 44262 44441 44441 44441 44262 44262 44441 44441 44441 44265 44262 44262 44262 44262 44263 44263 44263 44263 44262 44262 44262 44262 44262 44262 44262 44262 44441 44441 44441 44263 44263"
## [5] "PMC8082814 /pmc/articles/PMC8082814/bin/13059_2021_2334_MOESM3_ESM.xlsx Hsapiens 9 44441 44441 44441 44441 44441 44257 44264 44441 44264"
## [6] "PMC8082814 /pmc/articles/PMC8082814/bin/13059_2021_2334_MOESM3_ESM.xlsx Hsapiens 41 44441 44441 44441 44441 44441 44441 44441 44441 44441 44441 44441 44441 44441 44441 44441 44441 44441 44441 44441 44441 44441 44441 44441 44441 44441 44441 44441 44441 44441 44441 44441 44441 44441 44441 44441 44441 44441 44441 44441 44441 44441"
## [7] "PMC8082497 /pmc/articles/PMC8082497/bin/Table_1.XLSX Ggallus 5 43717 43525 43717 43717 43800"
## [8] "PMC8082497 /pmc/articles/PMC8082497/bin/Table_4.XLSX Hsapiens 2 43800 43527"
## [9] "PMC8079172 /pmc/articles/PMC8079172/bin/mmc6.xlsx Athaliana 1 44108"
## [10] "PMC8072132 /pmc/articles/PMC8072132/bin/mmc2.xlsx Mmusculus 27 38047 38961 37135 39873 38596 40422 39508 37865 40057 40238 38412 39326 36951 36951 40603 38777 38231 37500 42248 40787 37316 39142 39692 37681 37316 41883 41153"
## [11] "PMC8072132 /pmc/articles/PMC8072132/bin/mmc2.xlsx Mmusculus 3 37135 40422 40057"
## [12] "PMC8072132 /pmc/articles/PMC8072132/bin/mmc8.xlsx Hsapiens 1 44440"
## [13] "PMC8079977 /pmc/articles/PMC8079977/bin/Table_5.xlsx Scerevisiae 3 36982 39326 36982"
## [14] "PMC8078050 /pmc/articles/PMC8078050/bin/mmc8.xlsx Hsapiens 1 37165"
## [15] "PMC8054196 /pmc/articles/PMC8054196/bin/jitc-2020-002071supp004.xlsx Hsapiens 1 2021/09/14"
## [16] "PMC8072452 /pmc/articles/PMC8072452/bin/Table_1.xlsx Mmusculus 17 43892 43898 44081 43897 43895 43896 43892 44083 44085 44080 43899 44082 44089 43899 44083 44083 44079"
## [17] "PMC8072156 /pmc/articles/PMC8072156/bin/Table_1.xls Hsapiens 3 44083 44082 43891"
## [18] "PMC8071957 /pmc/articles/PMC8071957/bin/Table_3.xls Hsapiens 3 44447 44450 44446"
## [19] "PMC8064208 /pmc/articles/PMC8064208/bin/aging-13-202950-s030.xlsx Hsapiens 15 37104 42248 38231 37135 40057 37469 41153 37500 39326 40787 40422 37834 38200 39692 37865"
## [20] "PMC8064208 /pmc/articles/PMC8064208/bin/aging-13-202950-s031.xlsx Hsapiens 15 37469 40057 40422 38231 38596 37500 41153 37865 39326 40787 37135 37104 37834 39692 38200"
## [21] "PMC8064208 /pmc/articles/PMC8064208/bin/aging-13-202950-s032.xlsx Hsapiens 14 37104 37469 39692 40787 37865 37135 37500 38231 39326 38200 40422 37834 41153 40057"
## [22] "PMC8062533 /pmc/articles/PMC8062533/bin/41598_2021_88003_MOESM5_ESM.xlsx Rnorvegicus 59 38047 39142 40787 40787 38412 39692 39508 37500 37316 40422 39508 37135 39692 39326 38596 39508 37865 40238 38961 38596 37681 40603 38231 40422 40057 41883 39326 37316 39692 37316 37681 39142 39326 38777 36951 41153 36951 40238 39508 39508 41883 41883 38231 38231 38231 38231 38231 38231 38231 38231 38231 38231 38231 37316 38961 38961 38961 38961 38961"
## [23] "PMC8062533 /pmc/articles/PMC8062533/bin/41598_2021_88003_MOESM6_ESM.xlsx Rnorvegicus 17 43715 43713 43529 43716 43717 43712 43717 43526 43709 43723 43719 43527 43535 43717 43710 43715 43531"
## [24] "PMC8062533 /pmc/articles/PMC8062533/bin/41598_2021_88003_MOESM6_ESM.xlsx Mmusculus 14 39326 40057 37500 37316 38231 37135 38412 39692 40238 40787 39142 37316 37681 40603"
## [25] "PMC8060030 /pmc/articles/PMC8060030/bin/elife-67275-supp2.xlsx Dmelanogaster 10 43435 43345 43344 43435 43345 43344 43345 43344 43347 43345"
## [26] "PMC8056605 /pmc/articles/PMC8056605/bin/12859_2021_4126_MOESM6_ESM.xlsx Hsapiens 8 43898 44085 44083 43895 44076 43900 44081 44079"
## [27] "PMC8056605 /pmc/articles/PMC8056605/bin/12859_2021_4126_MOESM6_ESM.xlsx Hsapiens 8 44083 43895 44085 43900 44076 44081 43898 44079"
## [28] "PMC8056605 /pmc/articles/PMC8056605/bin/12859_2021_4126_MOESM6_ESM.xlsx Hsapiens 1 44083"
## [29] "PMC8052759 /pmc/articles/PMC8052759/bin/41065_2021_176_MOESM2_ESM.xls Hsapiens 3 2021/09/09 2021/09/06 2021/09/01"
## [30] "PMC8052759 /pmc/articles/PMC8052759/bin/41065_2021_176_MOESM3_ESM.xls Hsapiens 4 2021/09/09 2021/09/06 2021/09/01 2021/03/01"
## [31] "PMC8052759 /pmc/articles/PMC8052759/bin/41065_2021_176_MOESM4_ESM.xls Hsapiens 4 2021/09/09 2021/09/06 2021/03/01 2021/09/01"
## [32] "PMC8052083 /pmc/articles/PMC8052083/bin/medi-100-e25374-s001.xls Hsapiens 7 2019/03/04 2019/09/14 2019/12/01 2019/09/03 2019/09/05 2019/09/12 2019/03/10"
## [33] "PMC8050920 /pmc/articles/PMC8050920/bin/12915_2021_1011_MOESM5_ESM.xls Hsapiens 4 43898 44088 44080 44083"
## [34] "PMC8050920 /pmc/articles/PMC8050920/bin/12915_2021_1011_MOESM6_ESM.xls Hsapiens 2 44531 44259"
## [35] "PMC8050920 /pmc/articles/PMC8050920/bin/12915_2021_1011_MOESM6_ESM.xls Hsapiens 1 44446"
## [36] "PMC8051109 /pmc/articles/PMC8051109/bin/12915_2021_1008_MOESM1_ESM.xlsx Celegans 7 43896 43893 44075 43895 43983 43894 43892"
## [37] "PMC8051109 /pmc/articles/PMC8051109/bin/12915_2021_1008_MOESM1_ESM.xlsx Celegans 4 43922 43983 43895 43894"
## [38] "PMC8051109 /pmc/articles/PMC8051109/bin/12915_2021_1008_MOESM3_ESM.xlsx Celegans 3 44260 44348 44259"
## [39] "PMC8048365 /pmc/articles/PMC8048365/bin/13059_2021_2325_MOESM11_ESM.xlsx Hsapiens 9 44108 44115 44106 44108 44110 44106 44108 44115 44110"
## [40] "PMC8048365 /pmc/articles/PMC8048365/bin/13059_2021_2325_MOESM5_ESM.xlsx Hsapiens 1 43894"
## [41] "PMC8048084 /pmc/articles/PMC8048084/bin/12864_2021_7581_MOESM2_ESM.xlsx Hsapiens 2 44080 43891"
## [42] "PMC8048360 /pmc/articles/PMC8048360/bin/12711_2021_628_MOESM3_ESM.xlsx Hsapiens 10 43892 44079 43895 44081 44083 43898 43892 44084 44085 43891"
## [43] "PMC8048283 /pmc/articles/PMC8048283/bin/13287_2021_2310_MOESM1_ESM.xlsx Hsapiens 25 43891 43891 43900 43901 43892 43893 43894 43895 43896 43897 43898 43899 44075 44084 44085 44086 44088 44076 44077 44078 44079 44080 44081 44082 44083"
## [44] "PMC8048283 /pmc/articles/PMC8048283/bin/13287_2021_2310_MOESM2_ESM.xlsx Hsapiens 25 43891 43891 43900 43901 43892 43893 43894 43895 43896 43897 43898 43899 44075 44084 44085 44086 44088 44076 44077 44078 44079 44080 44081 44082 44083"
## [45] "PMC8042104 /pmc/articles/PMC8042104/bin/41598_2021_86753_MOESM7_ESM.xlsx Dmelanogaster 1 44166"
## [46] "PMC8034727 /pmc/articles/PMC8034727/bin/pcbi.1008860.s006.xlsx Ggallus 11 37316 39142 39873 38047 36951 38777 39508 40238 37681 40603 38412"
## [47] "PMC8031408 /pmc/articles/PMC8031408/bin/pone.0249773.s002.xlsx Hsapiens 3 43681 43679 43680"
## [48] "PMC8024315 /pmc/articles/PMC8024315/bin/42003_2021_1970_MOESM8_ESM.xlsx Hsapiens 17 44256 44257 44257 44260 44261 44264 44440 44449 44450 44441 44442 44443 44444 44445 44446 44447 44448"
## [49] "PMC8024315 /pmc/articles/PMC8024315/bin/42003_2021_1970_MOESM8_ESM.xlsx Hsapiens 18 44256 44257 44256 44257 44260 44261 44262 44264 44440 44449 44450 44441 44442 44444 44445 44446 44447 44448"
## [50] "PMC8022387 /pmc/articles/PMC8022387/bin/12868_2021_616_MOESM5_ESM.xlsx Rnorvegicus 20 40795 40795 40787 40613 40793 40790 40609 40791 40789 40793 40607 40797 40604 40801 40603 40795 40605 40610 40794 40788"
## [51] "PMC8025811 /pmc/articles/PMC8025811/bin/jitc-2020-002312supp002.xlsx Hsapiens 1 44088"
## [52] "PMC8025811 /pmc/articles/PMC8025811/bin/jitc-2020-002312supp002.xlsx Hsapiens 1 44088"
## [53] "PMC8046355 /pmc/articles/PMC8046355/bin/pcbi.1008890.s011.xlsx Mmusculus 21 42434 42625 42439 42431 42619 42624 42435 42625 42439 42431 42619 42624 42434 42622 42436 42617 42623 42620 42437 42628 42615"
## [54] "PMC8046355 /pmc/articles/PMC8046355/bin/pcbi.1008890.s011.xlsx Hsapiens 164 44080 44080 44080 44083 44083 44079 44083 44079 44083 44080 44079 44083 44083 44079 44083 44080 44083 44080 44083 44080 44079 44079 44080 44080 44079 44080 44080 44083 44080 44079 44083 44079 44080 44079 44079 44083 44083 44083 44079 44079 44080 44083 44080 44079 44079 44080 44083 44083 44079 44079 44080 44083 44079 44080 44080 44080 44080 44083 44080 44083 44079 44083 44083 44080 44083 44079 44079 44080 44080 44080 44080 44083 44079 44083 44079 44079 44080 44079 44080 44083 44079 44079 44079 44080 44083 44079 44079 44079 44083 44083 44080 44083 44079 44079 44080 44083 44083 44079 44079 44080 44080 44080 44080 44079 44083 44080 44079 44083 44080 44079 44083 44080 44083 44080 44079 44083 44079 44080 44079 44080 44083 44079 44079 44083 44080 44079 44083 44083 44080 44080 44080 44080 44079 44080 44080 44083 44083 44083 44080 44083 44079 44080 44083 44079 44083 44079 44079 44083 44083 44083 44083 44083 44080 44079 44083 44080 44083 44080 44083 44079 44080 44079 44079 44083"
## [55] "PMC8017017 /pmc/articles/PMC8017017/bin/41467_2021_21917_MOESM4_ESM.xlsx Hsapiens 3 44266 44263 44258"
## [56] "PMC8017017 /pmc/articles/PMC8017017/bin/41467_2021_21917_MOESM4_ESM.xlsx Hsapiens 11 44166 44166 44166 44166 44166 44166 44166 44166 44166 43892 44166"
## [57] "PMC8017017 /pmc/articles/PMC8017017/bin/41467_2021_21917_MOESM4_ESM.xlsx Hsapiens 3 44166 44166 43891"
## [58] "PMC8016308 /pmc/articles/PMC8016308/bin/pone.0248905.s002.xlsx Hsapiens 4 41153 38231 37135 38961"
## [59] "PMC8045971 /pmc/articles/PMC8045971/bin/Table_1.xlsx Hsapiens 8 9-Sep 15-Sep 6-Sep 2-Sep 10-Sep 1-Sep 11-Sep 7-Sep"
## [60] "PMC8045971 /pmc/articles/PMC8045971/bin/Table_1.xlsx Hsapiens 7 15-Sep 1-Sep 6-Sep 11-Sep 7-Sep 2-Sep 9-Sep"
## [61] "PMC8045971 /pmc/articles/PMC8045971/bin/Table_3.xlsx Hsapiens 5 9-Sep 7-Sep 2-Sep 7-Sep 9-Sep"
## [62] "PMC8045971 /pmc/articles/PMC8045971/bin/Table_3.xlsx Hsapiens 5 2-Sep 9-Sep 7-Sep 7-Sep 9-Sep"
## [63] "PMC8044451 /pmc/articles/PMC8044451/bin/Table_3.xlsx Hsapiens 2 43898 44078"
## [64] "PMC8027763 /pmc/articles/PMC8027763/bin/Supplementary_Data2.xlsx Rnorvegicus 2 43900 43891"
## [65] "PMC8012360 /pmc/articles/PMC8012360/bin/41467_2021_22234_MOESM3_ESM.xlsx Mmusculus 21 43891 43892 43892 43893 43894 43895 43896 43897 43898 43899 44084 44085 44086 44088 44076 44078 44079 44080 44081 44082 44083"
## [66] "PMC8011181 /pmc/articles/PMC8011181/bin/12885_2021_8052_MOESM4_ESM.xlsx Hsapiens 1 44081"
## [67] "PMC8011181 /pmc/articles/PMC8011181/bin/12885_2021_8052_MOESM5_ESM.xlsx Hsapiens 9 44077 43894 44079 44078 43891 44082 44088 43893 44084"
## [68] "PMC8011181 /pmc/articles/PMC8011181/bin/12885_2021_8052_MOESM5_ESM.xlsx Hsapiens 9 44077 43894 44079 44078 43891 44082 44088 43893 44084"
## [69] "PMC8043114 /pmc/articles/PMC8043114/bin/Table_8.xlsx Hsapiens 17 37104 37865 38231 39326 37469 38961 37834 38200 40787 41153 41883 39692 37500 37135 40057 38596 40422"
## [70] "PMC8043114 /pmc/articles/PMC8043114/bin/Table_8.xlsx Hsapiens 17 37104 37865 38231 39326 37469 38961 37834 38200 40787 41153 41883 39692 37500 37135 40057 38596 40422"
## [71] "PMC8043114 /pmc/articles/PMC8043114/bin/Table_8.xlsx Hsapiens 3 37469 40787 37500"
## [72] "PMC8043114 /pmc/articles/PMC8043114/bin/Table_8.xlsx Hsapiens 1 37500"
## [73] "PMC8043114 /pmc/articles/PMC8043114/bin/Table_8.xlsx Hsapiens 2 37469 40787"
## [74] "PMC8043114 /pmc/articles/PMC8043114/bin/Table_8.xlsx Ggallus 3 39326 40787 40057"
## [75] "PMC8043114 /pmc/articles/PMC8043114/bin/Table_9.xlsx Hsapiens 2 37500 40787"
## [76] "PMC8043114 /pmc/articles/PMC8043114/bin/Table_9.xlsx Hsapiens 2 37500 40787"
## [77] "PMC8042384 /pmc/articles/PMC8042384/bin/Table_2.xlsx Hsapiens 1 44082"
## [78] "PMC8009959 /pmc/articles/PMC8009959/bin/41598_2021_86683_MOESM1_ESM.xlsx Hsapiens 6 44085 44085 44085 44085 44085 44085"
## [79] "PMC8033158 /pmc/articles/PMC8033158/bin/Table_2.xlsx Hsapiens 23 44447 44447 44454 44450 44445 44445 44446 44441 44448 44262 44257 44264 44264 44447 44449 44449 44448 44445 44448 44257 44257 44448 44450"
## [80] "PMC8033158 /pmc/articles/PMC8033158/bin/Table_3.xlsx Hsapiens 1 44447"
## [81] "PMC8033158 /pmc/articles/PMC8033158/bin/Table_4.xlsx Hsapiens 28 44449 44257 44446 44259 44263 44265 44440 44442 44264 44441 44454 44445 44257 44453 44451 44262 44261 44450 44531 44447 44258 44443 44266 44260 44256 44444 44256 44448"
## [82] "PMC8033158 /pmc/articles/PMC8033158/bin/Table_5.xlsx Hsapiens 6 44259 44265 44440 44442 44453 44451"
## [83] "PMC8033158 zip/╨┬╜и╬─╝■╝╨/4-Singlecox_BLCA_DFI_all.xlsx Hsapiens 1 44447"
## [84] "PMC8033158 zip/╨┬╜и╬─╝■╝╨/4-Singlecox_BLCA_OS_select.xlsx Hsapiens 1 44447"
## [85] "PMC8033158 zip/╨┬╜и╬─╝■╝╨/4-Singlecox_BLCA_OS_all.xlsx Hsapiens 1 44447"
## [86] "PMC8020666 /pmc/articles/PMC8020666/bin/pnas.2015855118.sd05.xlsx Hsapiens 1 43893"
## [87] "PMC8020666 /pmc/articles/PMC8020666/bin/pnas.2015855118.sd07.xlsx Hsapiens 1 44443"
## [88] "PMC8020666 /pmc/articles/PMC8020666/bin/pnas.2015855118.sd07.xlsx Hsapiens 1 44442"
## [89] "PMC8020666 /pmc/articles/PMC8020666/bin/pnas.2015855118.sd07.xlsx Hsapiens 2 44256 44442"
## [90] "PMC8020666 /pmc/articles/PMC8020666/bin/pnas.2015855118.sd09.xlsx Hsapiens 2 43893 43891"
## [91] "PMC8020666 /pmc/articles/PMC8020666/bin/pnas.2015855118.sd09.xlsx Hsapiens 1 44078"
## [92] "PMC8020666 /pmc/articles/PMC8020666/bin/pnas.2015855118.sd09.xlsx Hsapiens 1 44077"
## [93] "PMC8020666 /pmc/articles/PMC8020666/bin/pnas.2015855118.sd09.xlsx Hsapiens 1 43893"
## [94] "PMC8020666 /pmc/articles/PMC8020666/bin/pnas.2015855118.sd09.xlsx Hsapiens 1 44078"
## [95] "PMC8020666 /pmc/articles/PMC8020666/bin/pnas.2015855118.sd09.xlsx Hsapiens 1 43898"
## [96] "PMC8020666 /pmc/articles/PMC8020666/bin/pnas.2015855118.sd11.xlsx Hsapiens 1 44078"
## [97] "PMC8020666 /pmc/articles/PMC8020666/bin/pnas.2015855118.sd11.xlsx Hsapiens 2 43891 43892"
## [98] "PMC8020666 /pmc/articles/PMC8020666/bin/pnas.2015855118.sd11.xlsx Hsapiens 1 44077"
## [99] "PMC8020666 /pmc/articles/PMC8020666/bin/pnas.2015855118.sd11.xlsx Hsapiens 2 44078 44079"
## [100] "PMC8020666 /pmc/articles/PMC8020666/bin/pnas.2015855118.sd11.xlsx Hsapiens 3 43891 43892 44077"
## [101] "PMC8020666 /pmc/articles/PMC8020666/bin/pnas.2015855118.sd11.xlsx Hsapiens 1 44077"
## [102] "PMC8020666 /pmc/articles/PMC8020666/bin/pnas.2015855118.sd11.xlsx Hsapiens 2 44078 44079"
## [103] "PMC8020666 /pmc/articles/PMC8020666/bin/pnas.2015855118.sd11.xlsx Hsapiens 2 44079 43891"
## [104] "PMC8020666 /pmc/articles/PMC8020666/bin/pnas.2015855118.sd11.xlsx Hsapiens 1 43891"
## [105] "PMC8020666 /pmc/articles/PMC8020666/bin/pnas.2015855118.sd11.xlsx Hsapiens 2 44078 44079"
## [106] "PMC8020666 /pmc/articles/PMC8020666/bin/pnas.2015855118.sd11.xlsx Hsapiens 2 44079 43891"
## [107] "PMC8020666 /pmc/articles/PMC8020666/bin/pnas.2015855118.sd11.xlsx Hsapiens 1 43891"
## [108] "PMC7997954 /pmc/articles/PMC7997954/bin/41523_2021_237_MOESM2_ESM.xlsx Hsapiens 1 43899"
## [109] "PMC7997954 /pmc/articles/PMC7997954/bin/41523_2021_237_MOESM2_ESM.xlsx Hsapiens 1 43530"
## [110] "PMC7997954 /pmc/articles/PMC7997954/bin/41523_2021_237_MOESM2_ESM.xlsx Hsapiens 1 43891"
## [111] "PMC7994904 /pmc/articles/PMC7994904/bin/42003_2021_1929_MOESM4_ESM.xlsx Hsapiens 13 43800 43720 43717 43529 43713 43718 43716 43530 43722 43531 43711 43712 43719"
## [112] "PMC7994904 /pmc/articles/PMC7994904/bin/42003_2021_1929_MOESM4_ESM.xlsx Hsapiens 11 43717 43800 43715 43532 43722 43720 43527 43719 43529 43711 43712"
## [113] "PMC7994904 /pmc/articles/PMC7994904/bin/42003_2021_1929_MOESM4_ESM.xlsx Hsapiens 13 43720 43532 43534 43528 43714 43530 43719 43711 43716 43718 43531 43715 43722"
## [114] "PMC7994904 /pmc/articles/PMC7994904/bin/42003_2021_1929_MOESM4_ESM.xlsx Hsapiens 12 43720 43717 43532 43710 43800 43530 43723 43529 43719 43533 43535 43711"
## [115] "PMC8025671 /pmc/articles/PMC8025671/bin/Table_4.XLSX Hsapiens 2 44257 44258"
## [116] "PMC7990179 /pmc/articles/PMC7990179/bin/pgen.1009355.s011.xlsx Drerio 1 43525"
## [117] "PMC7990179 /pmc/articles/PMC7990179/bin/pgen.1009355.s011.xlsx Drerio 1 43525"
## [118] "PMC7985503 /pmc/articles/PMC7985503/bin/41398_2021_1288_MOESM4_ESM.xlsx Hsapiens 29 42248 37316 36951 40422 39142 38047 37500 40787 36951 38777 40603 37681 39692 39326 41883 37226 39508 38412 39873 41153 37135 37135 38231 40238 40057 37316 38596 37865 38961"
## [119] "PMC7985503 /pmc/articles/PMC7985503/bin/41398_2021_1288_MOESM4_ESM.xlsx Hsapiens 29 42248 37316 36951 40422 39142 38047 37500 40787 36951 38777 40603 37681 39692 39326 41883 37226 39508 38412 39873 41153 37135 37135 38231 40238 40057 37316 38596 37865 38961"
## [120] "PMC7985503 /pmc/articles/PMC7985503/bin/41398_2021_1288_MOESM4_ESM.xlsx Hsapiens 29 42248 37316 36951 40422 39142 38047 37500 40787 36951 38777 40603 37681 39692 39326 41883 37226 39508 38412 39873 41153 37135 37135 38231 40238 40057 37316 38596 37865 38961"
## [121] "PMC7985503 /pmc/articles/PMC7985503/bin/41398_2021_1288_MOESM4_ESM.xlsx Hsapiens 29 42248 37316 36951 40422 39142 38047 37500 40787 36951 38777 40603 37681 39692 39326 41883 37226 39508 38412 39873 41153 37135 37135 38231 40238 40057 37316 38596 37865 38961"
## [122] "PMC7985503 /pmc/articles/PMC7985503/bin/41398_2021_1288_MOESM4_ESM.xlsx Hsapiens 29 42248 37316 36951 40422 39142 38047 37500 40787 36951 38777 40603 37681 39692 39326 41883 37226 39508 38412 39873 41153 37135 37135 38231 40238 40057 37316 38596 37865 38961"
## [123] "PMC7985503 /pmc/articles/PMC7985503/bin/41398_2021_1288_MOESM4_ESM.xlsx Hsapiens 29 42248 37316 36951 40422 39142 38047 37500 40787 36951 38777 40603 37681 39692 39326 41883 37226 39508 38412 39873 41153 37135 37135 38231 40238 40057 37316 38596 37865 38961"
## [124] "PMC7985503 /pmc/articles/PMC7985503/bin/41398_2021_1288_MOESM4_ESM.xlsx Hsapiens 29 42248 37316 36951 40422 39142 38047 37500 40787 36951 38777 40603 37681 39692 39326 41883 37226 39508 38412 39873 41153 37135 37135 38231 40238 40057 37316 38596 37865 38961"
## [125] "PMC7985503 /pmc/articles/PMC7985503/bin/41398_2021_1288_MOESM4_ESM.xlsx Hsapiens 29 42248 37316 36951 40422 39142 38047 37500 40787 36951 38777 40603 37681 39692 39326 41883 37226 39508 38412 39873 41153 37135 37135 38231 40238 40057 37316 38596 37865 38961"
## [126] "PMC7985503 /pmc/articles/PMC7985503/bin/41398_2021_1288_MOESM4_ESM.xlsx Hsapiens 29 42248 37316 36951 40422 39142 38047 37500 40787 36951 38777 40603 37681 39692 39326 41883 37226 39508 38412 39873 41153 37135 37135 38231 40238 40057 37316 38596 37865 38961"
## [127] "PMC7985503 /pmc/articles/PMC7985503/bin/41398_2021_1288_MOESM4_ESM.xlsx Hsapiens 29 42248 37316 36951 40422 39142 38047 37500 40787 36951 38777 40603 37681 39692 39326 41883 37226 39508 38412 39873 41153 37135 37135 38231 40238 40057 37316 38596 37865 38961"
## [128] "PMC7985503 /pmc/articles/PMC7985503/bin/41398_2021_1288_MOESM4_ESM.xlsx Hsapiens 29 42248 37316 36951 40422 39142 38047 37500 40787 36951 38777 40603 37681 39692 39326 41883 37226 39508 38412 39873 41153 37135 37135 38231 40238 40057 37316 38596 37865 38961"
## [129] "PMC7985503 /pmc/articles/PMC7985503/bin/41398_2021_1288_MOESM4_ESM.xlsx Hsapiens 29 42248 37316 36951 40422 39142 38047 37500 40787 36951 38777 40603 37681 39692 39326 41883 37226 39508 38412 39873 41153 37135 37135 38231 40238 40057 37316 38596 37865 38961"
## [130] "PMC7985503 /pmc/articles/PMC7985503/bin/41398_2021_1288_MOESM4_ESM.xlsx Hsapiens 29 42248 37316 36951 40422 39142 38047 37500 40787 36951 38777 40603 37681 39692 39326 41883 37226 39508 38412 39873 41153 37135 37135 38231 40238 40057 37316 38596 37865 38961"
## [131] "PMC7985503 /pmc/articles/PMC7985503/bin/41398_2021_1288_MOESM4_ESM.xlsx Hsapiens 29 42248 37316 36951 40422 39142 38047 37500 40787 36951 38777 40603 37681 39692 39326 41883 37226 39508 38412 39873 41153 37135 37135 38231 40238 40057 37316 38596 37865 38961"
## [132] "PMC7985503 /pmc/articles/PMC7985503/bin/41398_2021_1288_MOESM4_ESM.xlsx Hsapiens 29 42248 37316 36951 40422 39142 38047 37500 40787 36951 38777 40603 37681 39692 39326 41883 37226 39508 38412 39873 41153 37135 37135 38231 40238 40057 37316 38596 37865 38961"
## [133] "PMC7985503 /pmc/articles/PMC7985503/bin/41398_2021_1288_MOESM4_ESM.xlsx Hsapiens 29 42248 37316 36951 40422 39142 38047 37500 40787 36951 38777 40603 37681 39692 39326 41883 37226 39508 38412 39873 41153 37135 37135 38231 40238 40057 37316 38596 37865 38961"
## [134] "PMC7985503 /pmc/articles/PMC7985503/bin/41398_2021_1288_MOESM4_ESM.xlsx Hsapiens 29 42248 37316 36951 40422 39142 38047 37500 40787 36951 38777 40603 37681 39692 39326 41883 37226 39508 38412 39873 41153 37135 37135 38231 40238 40057 37316 38596 37865 38961"
## [135] "PMC7985503 /pmc/articles/PMC7985503/bin/41398_2021_1288_MOESM4_ESM.xlsx Hsapiens 29 42248 37316 36951 40422 39142 38047 37500 40787 36951 38777 40603 37681 39692 39326 41883 37226 39508 38412 39873 41153 37135 37135 38231 40238 40057 37316 38596 37865 38961"
## [136] "PMC7985503 /pmc/articles/PMC7985503/bin/41398_2021_1288_MOESM4_ESM.xlsx Hsapiens 29 42248 37316 36951 40422 39142 38047 37500 40787 36951 38777 40603 37681 39692 39326 41883 37226 39508 38412 39873 41153 37135 37135 38231 40238 40057 37316 38596 37865 38961"
## [137] "PMC7985503 /pmc/articles/PMC7985503/bin/41398_2021_1288_MOESM4_ESM.xlsx Hsapiens 29 42248 37316 36951 40422 39142 38047 37500 40787 36951 38777 40603 37681 39692 39326 41883 37226 39508 38412 39873 41153 37135 37135 38231 40238 40057 37316 38596 37865 38961"
## [138] "PMC7985503 /pmc/articles/PMC7985503/bin/41398_2021_1288_MOESM4_ESM.xlsx Hsapiens 29 42248 37316 36951 40422 39142 38047 37500 40787 36951 38777 40603 37681 39692 39326 41883 37226 39508 38412 39873 41153 37135 37135 38231 40238 40057 37316 38596 37865 38961"
## [139] "PMC7985503 /pmc/articles/PMC7985503/bin/41398_2021_1288_MOESM4_ESM.xlsx Hsapiens 29 42248 37316 36951 40422 39142 38047 37500 40787 36951 38777 40603 37681 39692 39326 41883 37226 39508 38412 39873 41153 37135 37135 38231 40238 40057 37316 38596 37865 38961"
## [140] "PMC7985503 /pmc/articles/PMC7985503/bin/41398_2021_1288_MOESM4_ESM.xlsx Hsapiens 29 42248 37316 36951 40422 39142 38047 37500 40787 36951 38777 40603 37681 39692 39326 41883 37226 39508 38412 39873 41153 37135 37135 38231 40238 40057 37316 38596 37865 38961"
## [141] "PMC7985503 /pmc/articles/PMC7985503/bin/41398_2021_1288_MOESM4_ESM.xlsx Hsapiens 29 42248 37316 36951 40422 39142 38047 37500 40787 36951 38777 40603 37681 39692 39326 41883 37226 39508 38412 39873 41153 37135 37135 38231 40238 40057 37316 38596 37865 38961"
## [142] "PMC7985503 /pmc/articles/PMC7985503/bin/41398_2021_1288_MOESM4_ESM.xlsx Hsapiens 29 42248 37316 36951 40422 39142 38047 37500 40787 36951 38777 40603 37681 39692 39326 41883 37226 39508 38412 39873 41153 37135 37135 38231 40238 40057 37316 38596 37865 38961"
## [143] "PMC7985503 /pmc/articles/PMC7985503/bin/41398_2021_1288_MOESM4_ESM.xlsx Hsapiens 29 42248 37316 36951 40422 39142 38047 37500 40787 36951 38777 40603 37681 39692 39326 41883 37226 39508 38412 39873 41153 37135 37135 38231 40238 40057 37316 38596 37865 38961"
## [144] "PMC7985195 /pmc/articles/PMC7985195/bin/42003_2021_1911_MOESM3_ESM.xlsx Hsapiens 1 43349"
## [145] "PMC7985195 /pmc/articles/PMC7985195/bin/42003_2021_1911_MOESM5_ESM.xlsx Hsapiens 27 44077 43897 43891 43901 43894 44088 44076 43893 44086 43896 44078 44082 44085 43892 44081 44084 43899 43891 44079 44083 43900 43898 43892 44166 44080 44075 43895"
## [146] "PMC7985195 /pmc/articles/PMC7985195/bin/42003_2021_1911_MOESM5_ESM.xlsx Hsapiens 27 43161 43346 43347 43161 43350 43349 43166 43354 43168 43355 43163 43160 43165 43357 43351 43167 43345 43435 43169 43162 43344 43170 43352 43348 43160 43353 43164"
## [147] "PMC8059334 /pmc/articles/PMC8059334/bin/mmc2.xlsx Ggallus 12 44443 44448 44448 44448 44448 44448 44448 44448 44448 44448 44448 44444"
## [148] "PMC8011804 /pmc/articles/PMC8011804/bin/pgen.1009443.s030.xlsx Hsapiens 8 40057 40057 40057 38047 40057 40057 40057 40057"
## [149] "PMC8011804 /pmc/articles/PMC8011804/bin/pgen.1009443.s031.xlsx Hsapiens 11 40057 40057 40057 40057 40057 40057 40057 40057 40057 40057 38047"
## [150] "PMC7979861 /pmc/articles/PMC7979861/bin/41467_2021_21798_MOESM4_ESM.xlsx Hsapiens 1 44089"
## [151] "PMC7979819 /pmc/articles/PMC7979819/bin/41467_2021_21883_MOESM8_ESM.xlsx Hsapiens 25 43525 43527 43527 43528 43529 43530 43530 43532 43532 43533 43718 43719 43710 43710 43711 43711 43712 43717 43717 43717 43717 43717 43717 43717 43710"
## [152] "PMC7979819 /pmc/articles/PMC7979819/bin/41467_2021_21883_MOESM8_ESM.xlsx Hsapiens 22 43718 43710 43717 43717 43527 43717 43717 43717 43717 43717 43715 43714 43718 43526 43715 43715 43715 43715 43713 43711 43711 43711"
## [153] "PMC7979819 /pmc/articles/PMC7979819/bin/41467_2021_21883_MOESM8_ESM.xlsx Hsapiens 2 43527 43527"
## [154] "PMC7979819 /pmc/articles/PMC7979819/bin/41467_2021_21883_MOESM8_ESM.xlsx Hsapiens 1 43527"
## [155] "PMC7979819 /pmc/articles/PMC7979819/bin/41467_2021_21883_MOESM9_ESM.xlsx Hsapiens 28 43719 43532 43526 43525 43535 43709 43527 43716 43720 43528 43715 43710 43712 43800 43531 43717 43529 43534 43530 43533 43723 43718 43722 43711 43713 43714 43526 43525"
## [156] "PMC8012900 /pmc/articles/PMC8012900/bin/Table_2.xlsx Hsapiens 27 44442 44445 44256 44261 44260 44257 44258 44263 44256 44450 44444 44257 44440 44449 44447 44446 44264 44259 44262 44531 44265 44453 44441 44443 44448 44451 44266"
## [157] "PMC7971549 /pmc/articles/PMC7971549/bin/pgen.1008887.s022.xlsx Dmelanogaster 7 42247 42250 42250 42250 42250 42250 42250"
## [158] "PMC7993683 /pmc/articles/PMC7993683/bin/aging-13-202723-s012.xlsx Hsapiens 2 44080 44082"
## [159] "PMC8027276 /pmc/articles/PMC8027276/bin/mmc2.xlsx Scerevisiae 2 43975 44105"
## [160] "PMC8027276 /pmc/articles/PMC8027276/bin/mmc4.xlsx Scerevisiae 2 44105 43975"
## [161] "PMC8050775 /pmc/articles/PMC8050775/bin/mmc5.xlsx Hsapiens 2 43891 43892"
## [162] "PMC8031731 /pmc/articles/PMC8031731/bin/NIHMS1678407-supplement-Data_S1.xlsx Hsapiens 1 43891"
## [163] "PMC8031731 /pmc/articles/PMC8031731/bin/NIHMS1678407-supplement-Data_S2.xlsx Hsapiens 3 43891 43895 44083"
## [164] "PMC8061397 /pmc/articles/PMC8061397/bin/ADVS-8-2004320-s002.xlsx Hsapiens 7 42988 42989 42979 42795 42795 42980 42800"
## [165] "PMC8017720 /pmc/articles/PMC8017720/bin/pnas.2015654118.sd01.xlsx Hsapiens 20 43347 43348 43163 43344 43349 43168 43350 43352 43160 43346 43164 43162 43165 43355 43353 43357 43167 43161 43354 43345"
## [166] "PMC7790035 /pmc/articles/PMC7790035/bin/41398_2020_1142_MOESM1_ESM.xlsx Hsapiens 1 36951"
## [167] "PMC7790035 /pmc/articles/PMC7790035/bin/41398_2020_1142_MOESM1_ESM.xlsx Hsapiens 3 36951 36951 36951"
## [168] "PMC8054830 /pmc/articles/PMC8054830/bin/NIHMS1637640-supplement-1637640_SuppData3.xlsx Hsapiens 4 44166 44075 44078 44083"
## [169] "PMC8054830 /pmc/articles/PMC8054830/bin/NIHMS1637640-supplement-1637640_SuppData3.xlsx Hsapiens 24 43891 43892 43897 43894 44085 43891 43896 43901 43893 44082 44081 44088 44166 43898 43895 43899 44086 44075 44078 43900 44083 43892 44079 44077"
## [170] "PMC8054830 /pmc/articles/PMC8054830/bin/NIHMS1637640-supplement-1637640_SuppData3.xlsx Hsapiens 2 43800 43717"
## [171] "PMC8054830 /pmc/articles/PMC8054830/bin/NIHMS1637640-supplement-1637640_SuppData3.xlsx Hsapiens 21 43892 43891 43897 43894 43891 43896 43901 43893 44088 44166 43898 43895 43899 44086 44075 44078 43900 44083 43892 44079 44077"
## [172] "PMC8054830 /pmc/articles/PMC8054830/bin/NIHMS1637640-supplement-1637640_SuppData3.xlsx Hsapiens 21 44084 44076 44085 43896 43901 43893 44082 44081 44088 44166 43898 43895 43899 44086 44075 44078 43900 44083 43892 44079 44077"
## [173] "PMC8054830 /pmc/articles/PMC8054830/bin/NIHMS1637640-supplement-1637640_SuppData3.xlsx Hsapiens 15 43526 43525 43531 43528 43525 43530 43535 43527 43800 43532 43529 43533 43534 43526 43711"
## [174] "PMC8054830 /pmc/articles/PMC8054830/bin/NIHMS1637640-supplement-SuppData5.xlsx Hsapiens 25 43800 43525 43534 43535 43526 43527 43528 43529 43530 43531 43532 43533 43723 43709 43718 43719 43722 43710 43711 43712 43713 43714 43715 43716 43717"
## [175] "PMC8054830 /pmc/articles/PMC8054830/bin/NIHMS1637640-supplement-SuppData5.xlsx Hsapiens 21 43525 43526 43527 43528 43529 43530 43531 43532 43533 43723 43709 43718 43719 43710 43711 43712 43713 43714 43715 43716 43717"
## [176] "PMC7507402 /pmc/articles/PMC7507402/bin/MSB-16-e9828-s010.xlsx Scerevisiae 24 37165 45413 45413 37165 45413 37165 45413 45413 37165 37165 37165 37165 45413 37165 37165 37165 37165 45413 37165 37165 37165 45413 37165 45413"
## [177] "PMC7521923 /pmc/articles/PMC7521923/bin/elife-56793-fig1-data1.xlsx Hsapiens 2 43718 43719"
## [178] "PMC7521923 /pmc/articles/PMC7521923/bin/elife-56793-fig1-data1.xlsx Hsapiens 3 43894 44083 43892"
## [179] "PMC7993145 /pmc/articles/PMC7993145/bin/KEPI_A_1805678_SM2368.xlsx Hsapiens 38 44166 44081 44083 43891 43896 44083 44084 44085 43891 44080 44080 43894 44166 44166 44085 43897 44166 43891 43894 43895 43891 43894 44166 43891 43901 43891 44085 44166 43895 43891 43901 43896 43891 43891 43891 43897 44082 44083"
## [180] "PMC7993145 /pmc/articles/PMC7993145/bin/KEPI_A_1805678_SM2368.xlsx Hsapiens 53 44083 44083 44166 44076 44081 44083 43891 43896 44166 44083 44084 44079 44085 44080 44166 43894 44166 44166 44085 43897 44081 43901 43891 44088 44166 43894 43895 43894 44166 43891 43901 44079 43891 43901 44085 44166 43895 43891 43901 43891 44089 44081 44081 43891 43891 43897 44077 44089 44166 44083 44082 44083 44081"
## [181] "PMC7993145 /pmc/articles/PMC7993145/bin/KEPI_A_1805678_SM2368.xlsx Hsapiens 1 43896"
## [182] "PMC7993145 /pmc/articles/PMC7993145/bin/KEPI_A_1805678_SM2368.xlsx Hsapiens 36 43896 43891 43891 44076 44083 44083 44081 44081 43891 44089 44089 43891 43891 43897 44084 43891 44083 44166 43891 43891 43891 43891 44166 44085 43897 43891 43897 44082 43891 44085 43891 43891 43893 43891 43894 43891"
## [183] "PMC7993145 /pmc/articles/PMC7993145/bin/KEPI_A_1805678_SM2368.xlsx Hsapiens 41 43896 43891 44166 43891 43891 44076 43891 44083 44081 44083 44081 44081 44166 44079 43891 44089 44089 44084 43891 44083 44166 43891 43891 44166 43891 44166 43897 43891 43891 44083 44166 43897 44083 44082 43900 43891 44085 43891 43893 43891 43894"
## [184] "PMC7993145 /pmc/articles/PMC7993145/bin/KEPI_A_1805678_SM2368.xlsx Hsapiens 2 43896 43891"
## [185] "PMC7993145 /pmc/articles/PMC7993145/bin/KEPI_A_1805678_SM2368.xlsx Ggallus 46 43896 43891 43891 43891 44084 43891 43891 43891 44089 43897 43895 44089 43891 43891 43891 43891 43891 44084 43895 43891 43891 43891 43891 43891 44076 44083 44076 43891 44076 44076 44076 44076 44081 43891 43897 44081 44076 44083 44082 43891 43891 43891 44076 43891 43891 43891"
## [186] "PMC7993145 /pmc/articles/PMC7993145/bin/KEPI_A_1805678_SM2368.xlsx Hsapiens 49 43896 43891 43891 44084 43891 43891 44089 43897 43895 44089 43891 43891 43891 43891 44079 44084 44076 43895 43891 43891 43891 43900 44166 43891 44076 44076 44076 44083 44083 43900 44083 44076 44076 43891 44076 43891 43898 44081 44076 44081 44076 43897 44081 44083 44082 43891 44076 43891 43891"
## [187] "PMC7993145 /pmc/articles/PMC7993145/bin/KEPI_A_1805678_SM2368.xlsx Hsapiens 3 43896 43891 43891"
## [188] "PMC7993145 /pmc/articles/PMC7993145/bin/KEPI_A_1805678_SM2368.xlsx Hsapiens 32 44083 44166 43891 44166 43894 44166 44083 44083 44166 44085 44166 43901 44081 44166 44085 43894 43891 44080 43891 44084 44080 44085 44082 43891 43901 43891 43891 44083 44086 43891 43891 43896"
## [189] "PMC7993145 /pmc/articles/PMC7993145/bin/KEPI_A_1805678_SM2368.xlsx Hsapiens 9 44083 44081 44083 44081 43891 43897 44081 43900 44083"
## [190] "PMC7993145 /pmc/articles/PMC7993145/bin/KEPI_A_1805678_SM2368.xlsx Hsapiens 53 44083 44166 44083 44083 44166 43891 44166 43894 44081 44166 44083 44083 44166 44079 44085 43891 44084 44077 44166 43901 44081 44088 44166 44085 43891 44083 44089 43894 44083 44080 43901 43891 44079 44084 43897 44085 44081 44079 43891 43901 43900 44166 43901 43901 44080 43901 43900 44083 43891 43891 43891 44166 43896"
## [191] "PMC7993145 /pmc/articles/PMC7993145/bin/KEPI_A_1805678_SM2368.xlsx Hsapiens 4 44083 44166 44083 44083"
## [192] "PMC7993145 /pmc/articles/PMC7993145/bin/KEPI_A_1805678_SM2368.xlsx Hsapiens 33 44166 44083 44083 44166 44166 44166 43894 44085 44083 44085 43894 43891 44082 44166 44081 43892 43894 43897 43891 43893 43891 43891 43893 44080 43901 43901 44084 43893 43896 43891 43891 43891 43891"
## [193] "PMC7993145 /pmc/articles/PMC7993145/bin/KEPI_A_1805678_SM2368.xlsx Hsapiens 9 44083 44083 44081 43900 44081 44081 43891 43897 43900"
## [194] "PMC7993145 /pmc/articles/PMC7993145/bin/KEPI_A_1805678_SM2368.xlsx Hsapiens 52 44166 44083 44083 44166 44166 44166 44083 43894 44085 44081 44083 44083 44084 44085 44089 44166 43894 43891 44088 44081 44082 43900 44079 43891 44166 44081 44083 44081 43891 43901 44166 43892 43891 43894 43897 43897 43900 43893 43891 43893 43901 43901 43901 44077 44084 43891 43896 44083 44084 43901 43891 43900"
## [195] "PMC7993145 /pmc/articles/PMC7993145/bin/KEPI_A_1805678_SM2368.xlsx Hsapiens 7 44166 44083 44083 44166 44166 44166 44083"
## [196] "PMC7993145 /pmc/articles/PMC7993145/bin/KEPI_A_1805678_SM2368.xlsx Hsapiens 30 44083 44166 44166 44083 44166 44166 43891 44166 44085 43894 44083 43891 43894 43894 43901 43893 44086 43900 43891 43896 44084 44080 43901 44085 43891 44084 43893 43896 43891 43893"
## [197] "PMC7993145 /pmc/articles/PMC7993145/bin/KEPI_A_1805678_SM2368.xlsx Hsapiens 52 44083 44166 44166 44083 44083 44166 44083 44166 43891 44166 44081 44085 44079 43894 44088 44083 44089 43891 43894 43894 43901 44084 43891 43896 44083 43891 43901 43897 44084 43891 44166 43901 44083 43891 44166 44085 43891 43901 43900 44084 43891 44081 44081 43900 43894 43901 43894 43893 44166 43891 44084 43893"
## [198] "PMC7993145 /pmc/articles/PMC7993145/bin/KEPI_A_1805678_SM2368.xlsx Hsapiens 2 44083 44083"
## [199] "PMC7993145 /pmc/articles/PMC7993145/bin/KEPI_A_1805678_SM2368.xlsx Hsapiens 7 44083 44166 44083 44083 44166 44083 44166"
## [200] "PMC7993145 /pmc/articles/PMC7993145/bin/KEPI_A_1805678_SM2368.xlsx Hsapiens 33 44166 44083 44083 44166 44083 44166 44085 44080 43896 44085 43894 44081 44166 44166 43891 43891 44084 44166 43891 43897 43891 43894 43892 43896 44166 43891 43893 43892 43891 44081 43895 43901 43891"
## [201] "PMC7993145 /pmc/articles/PMC7993145/bin/KEPI_A_1805678_SM2368.xlsx Hsapiens 45 44166 44083 44083 44166 44083 44166 44085 44080 44083 43896 44085 43894 44081 44166 44166 44081 44166 43891 44084 44166 44076 43897 44088 43891 43891 44166 43894 43891 43892 44081 44084 44081 44166 43891 44089 43891 43901 43891 43891 44081 43895 43901 43891 44089 43891"
## [202] "PMC7993145 /pmc/articles/PMC7993145/bin/KEPI_A_1805678_SM2368.xlsx Hsapiens 5 44166 44083 44083 44166 44083"
## [203] "PMC7993145 /pmc/articles/PMC7993145/bin/KEPI_A_1805678_SM2368.xlsx Hsapiens 34 44083 44166 44085 43891 43896 44083 44083 44166 44081 43891 44166 44166 44080 43897 43894 43893 44084 44081 44166 43894 44166 43891 43891 43894 44080 43891 43891 43891 43901 43891 44089 43895 43891 43891"
## [204] "PMC7993145 /pmc/articles/PMC7993145/bin/KEPI_A_1805678_SM2368.xlsx Hsapiens 50 44083 44083 44166 44085 44166 43891 43896 44076 44083 44083 44166 44081 44166 44166 44079 44080 44081 43897 43894 44084 44088 44081 44166 43901 43891 43894 44166 44166 44166 43891 43891 43894 43891 43901 43894 43891 43891 44089 43891 43901 43891 44089 43891 43895 44084 43891 44166 44081 44081 43891"
## [205] "PMC7993145 /pmc/articles/PMC7993145/bin/KEPI_A_1805678_SM2368.xlsx Hsapiens 5 44083 44083 44166 44085 44166"
## [206] "PMC7993145 /pmc/articles/PMC7993145/bin/KEPI_A_1805678_SM2368.xlsx Ggallus 36 44081 44166 44084 43891 44083 44085 44089 43896 43897 44089 43896 44166 44080 43891 43891 44166 44166 43891 43891 44084 44166 44083 43894 44076 44083 44085 44085 43895 43891 44083 44166 44089 43891 43895 44166 44076"
## [207] "PMC7993145 /pmc/articles/PMC7993145/bin/KEPI_A_1805678_SM2368.xlsx Hsapiens 45 44081 44166 44166 44084 44081 43891 44083 44083 44085 43891 44089 44166 43896 43897 44089 44166 44080 43891 43901 43891 44166 44081 44166 44083 44084 44166 44076 44083 43894 44083 44085 43895 43891 44166 43891 44079 44083 44166 44089 43895 43891 44166 44076 43901 44083"
## [208] "PMC7993145 /pmc/articles/PMC7993145/bin/KEPI_A_1805678_SM2368.xlsx Hsapiens 2 44081 44166"
## [209] "PMC7993145 /pmc/articles/PMC7993145/bin/KEPI_A_1805678_SM2368.xlsx Hsapiens 24 43896 44083 43896 44081 44080 43891 44084 44083 44166 43894 44166 44089 43893 44166 44076 44081 44085 43891 44085 44166 43895 43891 44084 44076"
## [210] "PMC7993145 /pmc/articles/PMC7993145/bin/KEPI_A_1805678_SM2368.xlsx Hsapiens 31 43896 44166 44083 43901 44081 44080 43891 44084 44083 44083 44166 43894 44083 44166 44089 44166 44076 44081 43891 44079 44085 43891 44085 44166 44080 43895 43891 43900 44084 44079 44089"
## [211] "PMC7567904 /pmc/articles/PMC7567904/bin/mmc3.xlsx Hsapiens 23 43525 43526 43718 43533 43525 43714 43713 43530 43527 43717 43716 43722 43710 43529 43532 43531 43719 43526 43711 43709 43715 43712 43534"
## [212] "PMC7610570 /pmc/articles/PMC7610570/bin/EMS118233-supplement-Dataset_1.xlsx Hsapiens 28 42248 37316 36951 39508 38412 39873 41153 37135 38231 40238 40057 37316 40422 39142 38047 37500 38596 37865 40787 36951 38777 40603 37681 39692 39326 41883 37226 38961"
## [213] "PMC7610570 /pmc/articles/PMC7610570/bin/EMS118233-supplement-Dataset_1.xlsx Hsapiens 28 42248 37316 36951 39508 38412 39873 41153 37135 38231 40238 40057 37316 40422 39142 38047 37500 38596 37865 40787 36951 38777 40603 37681 39692 39326 41883 37226 38961"
## [214] "PMC7610570 /pmc/articles/PMC7610570/bin/EMS118233-supplement-Dataset_1.xlsx Hsapiens 28 42248 37316 36951 39508 38412 39873 41153 37135 38231 40238 40057 37316 40422 39142 38047 37500 38596 37865 40787 36951 38777 40603 37681 39692 39326 41883 37226 38961"
## [215] "PMC7610570 /pmc/articles/PMC7610570/bin/EMS118233-supplement-Dataset_1.xlsx Hsapiens 28 42248 37316 36951 39508 38412 39873 41153 37135 38231 40238 40057 37316 40422 39142 38047 37500 38596 37865 40787 36951 38777 40603 37681 39692 39326 41883 37226 38961"
## [216] "PMC7610570 /pmc/articles/PMC7610570/bin/EMS118233-supplement-Dataset_1.xlsx Hsapiens 28 42248 37316 36951 39508 38412 39873 41153 37135 38231 40238 40057 37316 40422 39142 38047 37500 38596 37865 40787 36951 38777 40603 37681 39692 39326 41883 37226 38961"
## [217] "PMC7610570 /pmc/articles/PMC7610570/bin/EMS118233-supplement-Dataset_1.xlsx Hsapiens 28 42248 37316 36951 39508 38412 39873 41153 37135 38231 40238 40057 37316 40422 39142 38047 37500 38596 37865 40787 36951 38777 40603 37681 39692 39326 41883 37226 38961"
## [218] "PMC7610570 /pmc/articles/PMC7610570/bin/EMS118233-supplement-Dataset_2.xlsx Hsapiens 28 42248 37316 36951 39508 38412 39873 41153 37135 38231 40238 40057 37316 40422 39142 38047 37500 38596 37865 40787 36951 38777 40603 37681 39692 39326 41883 37226 38961"
## [219] "PMC8027439 /pmc/articles/PMC8027439/bin/41422_2020_385_MOESM10_ESM.xlsx Hsapiens 1 44079"
## [220] "PMC8019017 /pmc/articles/PMC8019017/bin/13238_2020_753_MOESM3_ESM.xlsx Hsapiens 23 42982 42798 42803 42799 42800 42981 42802 42984 42990 42805 42987 42993 42801 42986 42985 43070 42796 42988 42983 42980 42804 42989 42797"
## [221] "PMC8019017 /pmc/articles/PMC8019017/bin/13238_2020_753_MOESM3_ESM.xlsx Hsapiens 1 42982"
## [222] "PMC7608103 /pmc/articles/PMC7608103/bin/41422_2020_333_MOESM20_ESM.xlsx Hsapiens 1 43530"
## [223] "PMC7609296 /pmc/articles/PMC7609296/bin/41422_2020_322_MOESM14_ESM.xlsx Ggallus 1 43720"
## [224] "PMC7608117 /pmc/articles/PMC7608117/bin/41386_2020_643_MOESM6_ESM.xlsx Mmusculus 1 43530"
## [225] "PMC7608117 /pmc/articles/PMC7608117/bin/41386_2020_643_MOESM6_ESM.xlsx Mmusculus 3 43531 43713 43527"
## [226] "PMC7608117 /pmc/articles/PMC7608117/bin/41386_2020_643_MOESM6_ESM.xlsx Mmusculus 3 43535 43712 43713"
## [227] "PMC7608117 /pmc/articles/PMC7608117/bin/41386_2020_643_MOESM6_ESM.xlsx Mmusculus 6 43709 43528 43716 43712 43717 43535"
## [228] "PMC7608117 /pmc/articles/PMC7608117/bin/41386_2020_643_MOESM9_ESM.xlsx Rnorvegicus 1 43533"In depth look at the errors
Let’s investigate the errors in more detail.
# By species
SPECIES <- sapply(strsplit(ERROR_GENELISTS," "),"[[",3)
table(SPECIES)## SPECIES
## Athaliana Celegans Dmelanogaster Drerio Ggallus
## 1 3 3 2 7
## Hsapiens Mmusculus Rnorvegicus Scerevisiae
## 193 10 5 4par(mar=c(5,12,4,2))
barplot(table(SPECIES),horiz=TRUE,las=1)
par(mar=c(5,5,4,2))
# Number of affected Excel files per paper
DIST <- table(sapply(strsplit(ERROR_GENELISTS," "),"[[",1))
DIST##
## PMC7507402 PMC7521923 PMC7567904 PMC7608103 PMC7608117 PMC7609296 PMC7610570
## 1 2 1 1 5 1 7
## PMC7790035 PMC7971549 PMC7979819 PMC7979861 PMC7985195 PMC7985503 PMC7990179
## 2 1 5 1 3 26 2
## PMC7993145 PMC7993683 PMC7994904 PMC7997954 PMC8009959 PMC8011181 PMC8011804
## 32 1 4 3 1 3 2
## PMC8012360 PMC8012900 PMC8016308 PMC8017017 PMC8017720 PMC8019017 PMC8020666
## 1 1 1 3 1 2 22
## PMC8022387 PMC8024315 PMC8025671 PMC8025811 PMC8027276 PMC8027439 PMC8027763
## 1 2 1 2 2 1 1
## PMC8031408 PMC8031731 PMC8033158 PMC8034727 PMC8042104 PMC8042384 PMC8043114
## 1 2 7 1 1 1 8
## PMC8044451 PMC8045971 PMC8046355 PMC8048084 PMC8048283 PMC8048360 PMC8048365
## 1 4 2 1 2 1 2
## PMC8050775 PMC8050920 PMC8051109 PMC8052083 PMC8052759 PMC8054196 PMC8054830
## 1 3 3 1 3 1 8
## PMC8056605 PMC8059334 PMC8060030 PMC8061397 PMC8062533 PMC8064208 PMC8071957
## 3 1 1 1 3 3 1
## PMC8072132 PMC8072156 PMC8072452 PMC8078050 PMC8079172 PMC8079977 PMC8082497
## 3 1 1 1 1 1 2
## PMC8082814 PMC8082928
## 5 1summary(as.numeric(DIST))## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 1.000 1.000 1.500 3.167 3.000 32.000hist(DIST,main="Number of affected Excel files per paper")
# PMC Articles with the most errors
DIST_DF <- as.data.frame(DIST)
DIST_DF <- DIST_DF[order(-DIST_DF$Freq),,drop=FALSE]
head(DIST_DF,20)## Var1 Freq
## 15 PMC7993145 32
## 13 PMC7985503 26
## 28 PMC8020666 22
## 42 PMC8043114 8
## 56 PMC8054830 8
## 7 PMC7610570 7
## 38 PMC8033158 7
## 5 PMC7608117 5
## 10 PMC7979819 5
## 71 PMC8082814 5
## 17 PMC7994904 4
## 44 PMC8045971 4
## 12 PMC7985195 3
## 18 PMC7997954 3
## 20 PMC8011181 3
## 25 PMC8017017 3
## 51 PMC8050920 3
## 52 PMC8051109 3
## 54 PMC8052759 3
## 57 PMC8056605 3MOST_ERR_FILES = as.character(DIST_DF[1,1])
MOST_ERR_FILES## [1] "PMC7993145"# Number of errors per paper
NERR <- as.numeric(sapply(strsplit(ERROR_GENELISTS," "),"[[",4))
names(NERR) <- sapply(strsplit(ERROR_GENELISTS," "),"[[",1)
NERR <-tapply(NERR, names(NERR), sum)
NERR## PMC7507402 PMC7521923 PMC7567904 PMC7608103 PMC7608117 PMC7609296 PMC7610570
## 24 5 23 1 14 1 196
## PMC7790035 PMC7971549 PMC7979819 PMC7979861 PMC7985195 PMC7985503 PMC7990179
## 4 7 78 1 55 754 2
## PMC7993145 PMC7993683 PMC7994904 PMC7997954 PMC8009959 PMC8011181 PMC8011804
## 869 2 49 3 6 19 19
## PMC8012360 PMC8012900 PMC8016308 PMC8017017 PMC8017720 PMC8019017 PMC8020666
## 21 27 4 17 20 24 32
## PMC8022387 PMC8024315 PMC8025671 PMC8025811 PMC8027276 PMC8027439 PMC8027763
## 20 35 2 2 4 1 2
## PMC8031408 PMC8031731 PMC8033158 PMC8034727 PMC8042104 PMC8042384 PMC8043114
## 3 4 61 11 1 1 47
## PMC8044451 PMC8045971 PMC8046355 PMC8048084 PMC8048283 PMC8048360 PMC8048365
## 2 25 185 2 50 10 10
## PMC8050775 PMC8050920 PMC8051109 PMC8052083 PMC8052759 PMC8054196 PMC8054830
## 2 7 14 7 11 1 133
## PMC8056605 PMC8059334 PMC8060030 PMC8061397 PMC8062533 PMC8064208 PMC8071957
## 17 12 10 7 90 44 3
## PMC8072132 PMC8072156 PMC8072452 PMC8078050 PMC8079172 PMC8079977 PMC8082497
## 31 3 17 1 1 3 7
## PMC8082814 PMC8082928
## 85 1hist(NERR,main="number of errors per PMC article")
NERR_DF <- as.data.frame(NERR)
NERR_DF <- NERR_DF[order(-NERR_DF$NERR),,drop=FALSE]
head(NERR_DF,20)## NERR
## PMC7993145 869
## PMC7985503 754
## PMC7610570 196
## PMC8046355 185
## PMC8054830 133
## PMC8062533 90
## PMC8082814 85
## PMC7979819 78
## PMC8033158 61
## PMC7985195 55
## PMC8048283 50
## PMC7994904 49
## PMC8043114 47
## PMC8064208 44
## PMC8024315 35
## PMC8020666 32
## PMC8072132 31
## PMC8012900 27
## PMC8045971 25
## PMC7507402 24MOST_ERR = rownames(NERR_DF)[1]
MOST_ERR## [1] "PMC7993145"Journals affected
GENELIST_ERROR_ARTICLES <- gsub("PMC","",GENELIST_ERROR_ARTICLES)
### JSON PARSING is more reliable than XML
ARTICLES <- esummary( GENELIST_ERROR_ARTICLES , db="pmc" , retmode = "json" )
ARTICLE_DATA <- reutils::content(ARTICLES,as= "parsed")
ARTICLE_DATA <- ARTICLE_DATA$result
ARTICLE_DATA <- ARTICLE_DATA[2:length(ARTICLE_DATA)]
JOURNALS <- unlist(lapply(ARTICLE_DATA,function(x) {x$fulljournalname} ))
JOURNALS_TABLE <- table(JOURNALS)
JOURNALS_TABLE <- JOURNALS_TABLE[order(-JOURNALS_TABLE)]
length(JOURNALS_TABLE)## [1] 45par(mar=c(5,25,4,2))
barplot(head(JOURNALS_TABLE,10), horiz=TRUE, las=1,
xlab="Articles with gene name errors in supp files",
main="Top journals this month")
Journal of the month winner
Congrats to our Journal of the Month winner!
JOURNAL_WINNER <- names(head(JOURNALS_TABLE,1))
JOURNAL_WINNER## [1] "Frontiers in Oncology"Paper of the month winners
There are two categories:
Paper with the most suplementary files affected by gene name errors (MOST_ERR_FILES)
Paper with the most gene names converted to dates (MOST_ERR)
Sometimes, one paper can win both categories. Congrats to our winners.
Paper with most files affected
MOST_ERR_FILES <- gsub("PMC","",MOST_ERR_FILES)
ARTICLES <- esummary( MOST_ERR_FILES , db="pmc" , retmode = "json" )
ARTICLE_DATA <- reutils::content(ARTICLES,as= "parsed")
ARTICLE_DATA <- ARTICLE_DATA[2]
ARTICLE_DATA## $result
## $result$uids
## [1] "7993145"
##
## $result$`7993145`
## $result$`7993145`$uid
## [1] "7993145"
##
## $result$`7993145`$pubdate
## [1] "2020 Aug 25"
##
## $result$`7993145`$epubdate
## [1] "2020 Aug 25"
##
## $result$`7993145`$printpubdate
## [1] ""
##
## $result$`7993145`$source
## [1] "Epigenetics"
##
## $result$`7993145`$authors
## name authtype
## 1 Theisen ER Author
## 2 Selich-Anderson J Author
## 3 Miller KR Author
## 4 Tanner JM Author
## 5 Taslim C Author
## 6 Pishas KI Author
## 7 Sharma S Author
## 8 Lessnick SL Author
##
## $result$`7993145`$title
## [1] "Chromatin profiling reveals relocalization of lysine-specific demethylase 1 by an oncogenic fusion protein"
##
## $result$`7993145`$volume
## [1] "16"
##
## $result$`7993145`$issue
## [1] "4"
##
## $result$`7993145`$pages
## [1] "405-424"
##
## $result$`7993145`$articleids
## idtype value
## 1 pmid 32842875
## 2 doi 10.1080/15592294.2020.1805678
## 3 pmcid PMC7993145
##
## $result$`7993145`$fulljournalname
## [1] "Epigenetics"
##
## $result$`7993145`$sortdate
## [1] "2020/08/25 00:00"
##
## $result$`7993145`$pmclivedate
## [1] "2021/03/31"Paper with most date conversions
MOST_ERR <- gsub("PMC","",MOST_ERR)
ARTICLE_DATA <- esummary(MOST_ERR,db = "pmc" , retmode = "json" )
ARTICLE_DATA <- reutils::content(ARTICLE_DATA,as= "parsed")
ARTICLE_DATA## $header
## $header$type
## [1] "esummary"
##
## $header$version
## [1] "0.3"
##
##
## $result
## $result$uids
## [1] "7993145"
##
## $result$`7993145`
## $result$`7993145`$uid
## [1] "7993145"
##
## $result$`7993145`$pubdate
## [1] "2020 Aug 25"
##
## $result$`7993145`$epubdate
## [1] "2020 Aug 25"
##
## $result$`7993145`$printpubdate
## [1] ""
##
## $result$`7993145`$source
## [1] "Epigenetics"
##
## $result$`7993145`$authors
## name authtype
## 1 Theisen ER Author
## 2 Selich-Anderson J Author
## 3 Miller KR Author
## 4 Tanner JM Author
## 5 Taslim C Author
## 6 Pishas KI Author
## 7 Sharma S Author
## 8 Lessnick SL Author
##
## $result$`7993145`$title
## [1] "Chromatin profiling reveals relocalization of lysine-specific demethylase 1 by an oncogenic fusion protein"
##
## $result$`7993145`$volume
## [1] "16"
##
## $result$`7993145`$issue
## [1] "4"
##
## $result$`7993145`$pages
## [1] "405-424"
##
## $result$`7993145`$articleids
## idtype value
## 1 pmid 32842875
## 2 doi 10.1080/15592294.2020.1805678
## 3 pmcid PMC7993145
##
## $result$`7993145`$fulljournalname
## [1] "Epigenetics"
##
## $result$`7993145`$sortdate
## [1] "2020/08/25 00:00"
##
## $result$`7993145`$pmclivedate
## [1] "2021/03/31"Trend info
TODO: To plot the trend over the past 6 months.
References
Zeeberg, B.R., Riss, J., Kane, D.W. et al. Mistaken Identifiers: Gene name errors can be introduced inadvertently when using Excel in bioinformatics. BMC Bioinformatics 5, 80 (2004). https://doi.org/10.1186/1471-2105-5-80
Ziemann, M., Eren, Y. & El-Osta, A. Gene name errors are widespread in the scientific literature. Genome Biol 17, 177 (2016). https://doi.org/10.1186/s13059-016-1044-7
SessionInfo
sessionInfo()## R version 4.1.0 (2021-05-18)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.2 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
##
## locale:
## [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8
## [5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8
## [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] readxl_1.3.1 reutils_0.2.3 xml2_1.3.2 jsonlite_1.7.2
##
## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.6 knitr_1.33 magrittr_2.0.1 R6_2.5.0
## [5] rlang_0.4.11 stringr_1.4.0 highr_0.9 tools_4.1.0
## [9] xfun_0.23 jquerylib_0.1.4 htmltools_0.5.1.1 yaml_2.2.1
## [13] digest_0.6.27 assertthat_0.2.1 sass_0.4.0 bitops_1.0-7
## [17] RCurl_1.98-1.3 evaluate_0.14 rmarkdown_2.8 stringi_1.6.2
## [21] compiler_4.1.0 bslib_0.2.5.1 cellranger_1.1.0 XML_3.99-0.6