Source: https://github.com/markziemann/paddi-genomics

Workflow

if ( ! file.exists("qc.html") ) {  rmarkdown::render("qc.Rmd") }
## 
## 
## processing file: qc.Rmd
## 1/106                    
## 2/106 [libraries]        
## 3/106                    
## 4/106 [rrna]
## 5/106                    
## 6/106 [load]             
## 7/106                    
## 8/106 [numreads]
## 9/106                    
## 10/106 [mds1]
## 11/106                    
## 12/106 [mds2]
## 13/106                    
## 14/106 [loadpatientinfo]  
## 15/106                    
## 16/106 [mds3]
## 17/106                    
## 18/106 [pca1]
## 19/106                    
## 20/106 [pca]
## 21/106                    
## 22/106 [pcaplots]
## 23/106                    
## 24/106 [pcaplots_t0]
## 25/106                    
## 26/106 [pcaplots_eos]
## 27/106                    
## 28/106 [pcaplots_pod1]
## 29/106                    
## 30/106 [blood1]
## 31/106                    
## 32/106 [cells2]
## 33/106                    
## 34/106 [cells3]
## 35/106                    
## 36/106 [cellpca]
## 37/106                    
## 38/106 [crp_t0_1]         
## 39/106                    
## 40/106 [alox15b]
## 41/106                    
## 42/106 [crp_t0_2]         
## 43/106                    
## 44/106 [crp_eos]          
## 45/106                    
## 46/106 [crp_eos_viz]
## 47/106                    
## 48/106 [crp_pod1]         
## 49/106                    
## 50/106 [crp_pod1_viz]
## 51/106                    
## 52/106 [dex_t0]           
## 53/106                    
## 54/106 [dex_eos]          
## 55/106                    
## 56/106 [dex_pod1]         
## 57/106                    
## 58/106 [dex_crplo_t0]     
## 59/106                    
## 60/106 [dex_crphi_t0]     
## 61/106                    
## 62/106 [dex_crplo_eos]    
## 63/106                    
## 64/106 [save_dex_genes]
## 65/106                    
## 66/106 [baselineassocdex1]
## 67/106                    
## 68/106 [csmd1_check]
## 69/106                    
## 70/106 [dex_crphi_eos]    
## 71/106                    
## 72/106 [dex_crplo_pod]    
## 73/106                    
## 74/106 [dex_crphi_pod]    
## 75/106                    
## 76/106 [crp_t0_A]         
## 77/106                    
## 78/106 [crp_t0_B]         
## 79/106                    
## 80/106 [crp_eos_A]        
## 81/106                    
## 82/106 [crp_eos_B]        
## 83/106                    
## 84/106 [crp_pod1_A]       
## 85/106                    
## 86/106 [crp_pod1_B]       
## 87/106                    
## 88/106 [FvM_lowcrp_t0]    
## 89/106                    
## 90/106 [FvM_lowcrp_EOS]   
## 91/106                    
## 92/106 [FvM_lowcrp_POD]   
## 93/106                    
## 94/106 [FvM_hicrp_t0]     
## 95/106                    
## 96/106 [FvM_hicrp_eos]    
## 97/106                    
## 98/106 [FvM_hicrp_pod1]   
## 99/106                    
## 100/106 [surgfemale]       
## 101/106                    
## 102/106 [surgmale]         
## 103/106                    
## 104/106 [mf_compare]
## 105/106                    
## 106/106 [sessioninfo]
## output file: qc.knit.md
## /usr/bin/pandoc +RTS -K512m -RTS qc.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output qc.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/table-classes.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --syntax-highlighting=none --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpDuNPu1/rmarkdown-strbbb1297baf8.html
## 
## Output created: qc.html
if ( ! file.exists("qc_dge_infec.html") ) {  rmarkdown::render("qc_dge_infec.Rmd") }
## 
## 
## processing file: qc_dge_infec.Rmd
## 1/134                   
## 2/134 [libraries]       
## 3/134                   
## 4/134 [rrna]
## 5/134                   
## 6/134 [load]            
## 7/134                   
## 8/134 [numreads]
## 9/134                   
## 10/134 [mds1]
## 11/134                   
## 12/134 [mds2]
## 13/134                   
## 14/134 [loadpatientinfo] 
## 15/134                   
## 16/134 [pca1]
## 17/134                   
## 18/134 [pca]
## 19/134                   
## 20/134 [pcaplots]
## 21/134                   
## 22/134 [pcaplots_t0]
## 23/134                   
## 24/134 [pcaplots_eos]
## 25/134                   
## 26/134 [pcaplots_pod1]
## 27/134                   
## 28/134 [loadinfec]       
## 29/134                   
## 30/134 [pca_infec]
## 31/134                   
## 32/134 [blood1]
## 33/134                   
## 34/134 [cells2]
## 35/134                   
## 36/134 [cellpca]
## 37/134                   
## 38/134 [crp_t0]          
## 39/134                   
## 40/134 [crp_eos]         
## 41/134                   
## 42/134 [crp_pod1]        
## 43/134                   
## 44/134 [avb_t0]          
## 45/134                   
## 46/134 [avb_eos]         
## 47/134                   
## 48/134 [avb_pod1]        
## 49/134                   
## 50/134 [avb_crplo_t0]    
## 51/134                   
## 52/134 [avb_crphi_t0]    
## 53/134                   
## 54/134 [avb_crplo_eos]   
## 55/134                   
## 56/134 [avb_crphi_eos]   
## 57/134                   
## 58/134 [avb_crplo_pod]   
## 59/134                   
## 60/134 [avb_crphi_pod]   
## 61/134                   
## 62/134 [crp_t0_A]        
## 63/134                   
## 64/134 [crp_t0_B]        
## 65/134                   
## 66/134 [crp_eos_A]       
## 67/134                   
## 68/134 [crp_eos_B]       
## 69/134                   
## 70/134 [crp_pod1_A]      
## 71/134                   
## 72/134 [crp_pod1_B]      
## 73/134                   
## 74/134 [FvM_lowcrp_t0]   
## 75/134                   
## 76/134 [FvM_lowcrp_EOS]  
## 77/134                   
## 78/134 [FvM_lowcrp_POD]  
## 79/134                   
## 80/134 [FvM_hicrp_t0]    
## 81/134                   
## 82/134 [FvM_hicrp_eos]   
## 83/134                   
## 84/134 [FvM_hicrp_pod1]  
## 85/134                   
## 86/134 [surgfemale]      
## 87/134                   
## 88/134 [surgmale]        
## 89/134                   
## 90/134 [mf_compare]
## 91/134                   
## 92/134 [infec_t0]        
## 93/134                   
## 94/134 [infec_t0_box]
## 95/134                   
## 96/134 [infec_eos]       
## 97/134                   
## 98/134 [infec_eos_box]
## 99/134                   
## 100/134 [infec_pod1]      
## 101/134                   
## 102/134 [infec_pod1_box]
## 103/134                   
## 104/134 [infec_hi_t0]     
## 105/134                   
## 106/134 [infec_hi_eos]    
## 107/134                   
## 108/134 [infec_hi_pod1]   
## 109/134                   
## 110/134 [infec_lo_t0]     
## 111/134                   
## 112/134 [infec_lo_eos]    
## 113/134                   
## 114/134 [infec_lo_pod1]   
## 115/134                   
## 116/134 [infec_A_t0]      
## 117/134                   
## 118/134 [infec_A_eos]     
## 119/134                   
## 120/134 [infec_A_pod1]    
## 121/134                   
## 122/134 [infec_B_t0]      
## 123/134                   
## 124/134 [infec_B_eos]     
## 125/134                   
## 126/134 [infec_B_pod1]    
## 127/134                   
## 128/134 [blood_infec_t0]  
## 129/134                   
## 130/134 [blood_infec_eos] 
## 131/134                   
## 132/134 [blood_infec_pod1]
## 133/134                   
## 134/134 [sessioninfo]
## output file: qc_dge_infec.knit.md
## /usr/bin/pandoc +RTS -K512m -RTS qc_dge_infec.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output qc_dge_infec.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/table-classes.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --syntax-highlighting=none --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpDuNPu1/rmarkdown-strbbb6bde9970.html
## 
## Output created: qc_dge_infec.html
if ( ! file.exists("downstream.html") ) {  rmarkdown::render("downstream.Rmd") }

if ( ! file.exists("enrichment_reactome.html") ) {  rmarkdown::render("enrichment_reactome.Rmd") }
## 
## 
## processing file: enrichment_reactome.Rmd
## 1/22               
## 2/22 [libraries]   
## 3/22               
## 4/22 [geneset]     
## 5/22               
## 6/22 [genetable]   
## 7/22               
## 8/22 [mitch1]
## 9/22               
## 10/22 [interactions]
## 11/22               
## 12/22 [multi1]
## 13/22               
## 14/22 [multi1_t0]
## 15/22               
## 16/22 [mitch2]
## 17/22               
## 18/22 [multi2]
## 19/22               
## 20/22 [multi2_t0]
## 21/22               
## 22/22 [sessioninfo]
## output file: enrichment_reactome.knit.md
## /usr/bin/pandoc +RTS -K512m -RTS enrichment_reactome.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output enrichment_reactome.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/table-classes.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --syntax-highlighting=none --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpDuNPu1/rmarkdown-strbbbaf57e9b.html
## 
## Output created: enrichment_reactome.html
if ( ! file.exists("enrichment_go.html") ) {  rmarkdown::render("enrichment_go.Rmd") }
## 
## 
## processing file: enrichment_go.Rmd
## 1/20              
## 2/20 [libraries]  
## 3/20              
## 4/20 [geneset]    
## 5/20              
## 6/20 [genetable]  
## 7/20              
## 8/20 [mitch1]
## 9/20              
## 10/20 [multi1]
## 11/20              
## 12/20 [multi1_t0]
## 13/20              
## 14/20 [mitch2]
## 15/20              
## 16/20 [multi2]
## 17/20              
## 18/20 [multi2_t0]
## 19/20              
## 20/20 [sessioninfo]
## output file: enrichment_go.knit.md
## /usr/bin/pandoc +RTS -K512m -RTS enrichment_go.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output enrichment_go.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/table-classes.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --syntax-highlighting=none --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpDuNPu1/rmarkdown-strbbb43e06d48.html
## 
## Output created: enrichment_go.html
if ( ! file.exists("tca.html") ) {  rmarkdown::render("tca.Rmd") }
## 
## 
## processing file: tca.Rmd
## 1/56                    
## 2/56 [libraries]        
## 3/56                    
## 4/56 [load]             
## 5/56                    
## 6/56 [numreads]
## 7/56                    
## 8/56 [mds1]
## 9/56                    
## 10/56 [mds2]
## 11/56                    
## 12/56 [loadpatientinfo]  
## 13/56                    
## 14/56 [mds3]
## 15/56                    
## 16/56 [blood1]
## 17/56                    
## 18/56 [cells2]
## 19/56                    
## 20/56 [cellpca]
## 21/56                    
## 22/56 [tc_crplo]
## 23/56                    
## 24/56 [tc_crplo2]        
## 25/56                    
## 26/56 [tc_crplo3]        
## 27/56                    
## 28/56 [tc_crphi]
## 29/56                    
## 30/56 [tc_crphi_topgenes]
## 31/56                    
## 32/56 [tc_crphi2]        
## 33/56                    
## 34/56 [tc_crphi3]        
## 35/56                    
## 36/56 [tc_a]
## 37/56                    
## 38/56 [tc_a2]            
## 39/56                    
## 40/56 [tc_a3]            
## 41/56                    
## 42/56 [tc_b]
## 43/56                    
## 44/56 [tc_b2]            
## 45/56                    
## 46/56 [tc_b3]            
## 47/56                    
## 48/56 [tc_crplo_a]
## 49/56                    
## 50/56 [tc_crplo_b]
## 51/56                    
## 52/56 [tc_crphi_a]
## 53/56                    
## 54/56 [tc_crphi_b]
## 55/56                    
## 56/56 [sessioninfo]
## output file: tca.knit.md
## /usr/bin/pandoc +RTS -K512m -RTS tca.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output tca.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/table-classes.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --syntax-highlighting=none --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpDuNPu1/rmarkdown-strbbb7b2f4fe2.html
## 
## Output created: tca.html
if ( ! file.exists("tca_pairwise.html") ) {  rmarkdown::render("tca_pairwise.Rmd") }
## 
## 
## processing file: tca_pairwise.Rmd
## 1/62                      
## 2/62 [libraries]          
## 3/62                      
## 4/62 [load]               
## 5/62                      
## 6/62 [numreads]
## 7/62                      
## 8/62 [mds1]
## 9/62                      
## 10/62 [mds2]
## 11/62                      
## 12/62 [loadpatientinfo]    
## 13/62                      
## 14/62 [mds3]
## 15/62                      
## 16/62 [blood1]
## 17/62                      
## 18/62 [cells2]
## 19/62                      
## 20/62 [cellpca]
## 21/62                      
## 22/62 [blood2]
## 23/62                      
## 24/62 [tc_crplo_T0vEOS]    
## 25/62                      
## 26/62 [tc_crplo_EOSvPOD1]  
## 27/62                      
## 28/62 [tc_crplo_T0vPOD1]   
## 29/62                      
## 30/62 [tc_crphi_T0vEOS]    
## 31/62                      
## 32/62 [tc_crphi_EOSvPOD1]  
## 33/62                      
## 34/62 [tc_crphi_T0vPOD1]   
## 35/62                      
## 36/62 [tc_crplo_a_T0vEOS]  
## 37/62                      
## 38/62 [tc_crplo_a_EOSvPOD1]
## 39/62                      
## 40/62 [tc_crplo_a_T0vPOD1] 
## 41/62                      
## 42/62 [tc_crplo_b_T0vEOS]  
## 43/62                      
## 44/62 [tc_crplo_b_EOSvPOD1]
## 45/62                      
## 46/62 [tc_crplo_b_T0vPOD1] 
## 47/62                      
## 48/62 [tc_crphi_a_T0vEOS]  
## 49/62                      
## 50/62 [tc_crphi_a_EOSvPOD1]
## 51/62                      
## 52/62 [tc_crphi_a_T0vPOD1] 
## 53/62                      
## 54/62 [tc_crphi_b_T0vEOS]  
## 55/62                      
## 56/62 [tc_crphi_b_EOSvPOD1]
## 57/62                      
## 58/62 [tc_crphi_b_T0vPOD1] 
## 59/62                      
## 60/62 [tc_trtA_T0vEOS]     
## 61/62                      
## 62/62 [sessioninfo]
## output file: tca_pairwise.knit.md
## /usr/bin/pandoc +RTS -K512m -RTS tca_pairwise.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output tca_pairwise.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/table-classes.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --syntax-highlighting=none --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpDuNPu1/rmarkdown-strbbb5560a4be.html
## 
## Output created: tca_pairwise.html
if ( ! file.exists("tca_pairwise_downstream.html") ) {  rmarkdown::render("tca_pairwise_downstream.Rmd") }
## 
## 
## processing file: tca_pairwise_downstream.Rmd
## 1/52                  
## 2/52 [libraries]      
## 3/52                  
## 4/52 [load]           
## 5/52                  
## 6/52 [decompfunc]     
## 7/52                  
## 8/52 [quant1]         
## 9/52                  
## 10/52 [quant2]         
## 11/52                  
## 12/52 [quant3]         
## 13/52                  
## 14/52 [quant4]         
## 15/52                  
## 16/52 [quant5]         
## 17/52                  
## 18/52 [quant6]         
## 19/52                  
## 20/52 [cellcorrection]
## 21/52                  
## 22/52 [lowcrpquant]
## 23/52                  
## 24/52 [hicrpquant]
## 25/52                  
## 26/52 [lowcrp_a_quant]
## 27/52                  
## 28/52 [lowcrp_b_quant]
## 29/52                  
## 30/52 [hicrp_a_quant]
## 31/52                  
## 32/52 [hicrp_b_quant]
## 33/52                  
## 34/52 [t0veos_hilo]
## 35/52                  
## 36/52 [eosvpod1_hilo]
## 37/52                  
## 38/52 [tovpod1_hilo]
## 39/52                  
## 40/52 [lo_t0veos_avb]
## 41/52                  
## 42/52 [lo_eosvpod1_avb]
## 43/52                  
## 44/52 [lo_t0vpod1_avb]
## 45/52                  
## 46/52 [hi_t0veos_avb]
## 47/52                  
## 48/52 [hi_eosvpod1_avb]
## 49/52                  
## 50/52 [hi_t0vpod1_avb]
## 51/52                  
## 52/52 [sessioninfo]
## output file: tca_pairwise_downstream.knit.md
## /usr/bin/pandoc +RTS -K512m -RTS tca_pairwise_downstream.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output tca_pairwise_downstream.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/table-classes.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --syntax-highlighting=none --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpDuNPu1/rmarkdown-strbbb6ff8ab79.html
## 
## Output created: tca_pairwise_downstream.html
if ( ! file.exists("tca_pairwise_pathways.html") ) {  rmarkdown::render("tca_pairwise_pathways.Rmd") }
## 
## 
## processing file: tca_pairwise_pathways.Rmd
## 1/50                  
## 2/50 [libraries]      
## 3/50                  
## 4/50 [load]           
## 5/50                  
## 6/50 [mitchpwfuncs]   
## 7/50                  
## 8/50 [quant1]
## 9/50                  
## 10/50 [quant2]
## 11/50                  
## 12/50 [quant3]
## 13/50                  
## 14/50 [quant4]
## 15/50                  
## 16/50 [quant5]
## 17/50                  
## 18/50 [quant6]
## 19/50                  
## 20/50 [lowcrpquant]
## 21/50                  
## 22/50 [hicrpquant]
## 23/50                  
## 24/50 [lowcrp_a_quant]
## 25/50                  
## 26/50 [lowcrp_b_quant]
## 27/50                  
## 28/50 [hicrp_a_quant]
## 29/50                  
## 30/50 [hicrp_b_quant]
## 31/50                  
## 32/50 [t0veos_hilo]
## 33/50                  
## 34/50 [eosvpod1_hilo]
## 35/50                  
## 36/50 [tovpod1_hilo]
## 37/50                  
## 38/50 [lo_t0veos_avb]
## 39/50                  
## 40/50 [lo_eosvpod1_avb]
## 41/50                  
## 42/50 [lo_t0vpod1_avb]
## 43/50                  
## 44/50 [hi_t0veos_avb]
## 45/50                  
## 46/50 [hi_eosvpod1_avb]
## 47/50                  
## 48/50 [hi_t0vpod1_avb]
## 49/50                  
## 50/50 [sessioninfo]
## output file: tca_pairwise_pathways.knit.md
## /usr/bin/pandoc +RTS -K512m -RTS tca_pairwise_pathways.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output tca_pairwise_pathways.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/table-classes.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --syntax-highlighting=none --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpDuNPu1/rmarkdown-strbbb57d899d0.html
## 
## Output created: tca_pairwise_pathways.html
message("Done!")
## Done!