Rerun count-contributions analysis module (#1649)

Co-authored-by: GitHub Actions <actions@github.com>

analyses/count-contributions/03-set-authorship-order.nb.html

@@ -3084,7 +3084,7 @@ <h3>All positions and update metadata</h3>
 <!-- rnb-source-end -->
 <div data-pagedtable="false">
 <script data-pagedtable-source type="application/json">
-{"columns":[{"label":[""],"name":["_rn_"],"type":[""],"align":["left"]},{"label":["all_contributors_positions"],"name":[1],"type":["dbl"],"align":["right"]}],"data":[{"1":"1","_rn_":"Joshua A. Shapiro"},{"1":"2","_rn_":"Krutika S. Gaonkar"},{"1":"3","_rn_":"Candace L. Savonen"},{"1":"4","_rn_":"Stephanie J. Spielman"},{"1":"5","_rn_":"Chante J. Bethell"},{"1":"6","_rn_":"Run Jin"},{"1":"7","_rn_":"Komal S. Rathi"},{"1":"8","_rn_":"Yuankun Zhu"},{"1":"9","_rn_":"Laura E. Egolf"},{"1":"10","_rn_":"Bailey Farrow"},{"1":"11","_rn_":"Daniel P. Miller"},{"1":"12","_rn_":"Yang Yang"},{"1":"13","_rn_":"Tejaswi Koganti"},{"1":"14","_rn_":"Nighat Noureen"},{"1":"15","_rn_":"Mateusz P. Koptyra"},{"1":"16","_rn_":"Nhat Duong"},{"1":"17","_rn_":"Douglas R. Stewart"},{"1":"18","_rn_":"Angela J. Waanders"},{"1":"19","_rn_":"Nicholas Van Kuren"},{"1":"20","_rn_":"Yiran Guo"},{"1":"21","_rn_":"Javad Nazarian"},{"1":"22","_rn_":"Jena V. Lilly"},{"1":"23","_rn_":"Ashley S. Margol"},{"1":"24","_rn_":"Payal Jain"},{"1":"25","_rn_":"Stephen C. Mack"},{"1":"26","_rn_":"Zalman Vaksman"},{"1":"27","_rn_":"Jennifer L. Mason"},{"1":"28","_rn_":"Phillip B. Storm"},{"1":"29","_rn_":"Bailey K. Farrow"},{"1":"30","_rn_":"Rishi R. Lulla"},{"1":"31","_rn_":"Allison P. Heath"},{"1":"32","_rn_":"Adam A. Kraya"},{"1":"33","_rn_":"Brian R. Rood"},{"1":"34","_rn_":"Angela N. Viaene"},{"1":"35","_rn_":"Shannon Robins"},{"1":"36","_rn_":"Jung Kim"},{"1":"37","_rn_":"Hongbo M. Xie"},{"1":"38","_rn_":"Bo Zhang"},{"1":"39","_rn_":"Kristina A. Cole"},{"1":"40","_rn_":"Brian M. Ennis"},{"1":"41","_rn_":"Michael Prados"},{"1":"42","_rn_":"Rebecca S. Kaufman"},{"1":"43","_rn_":"Pichai Raman"},{"1":"44","_rn_":"Cassie Kline"},{"1":"45","_rn_":"Shrivats Kannan"},{"1":"46","_rn_":"Xiaoyan Huang"},{"1":"47","_rn_":"Steven M. Foltz"},{"1":"48","_rn_":"Sabine Mueller"},{"1":"49","_rn_":"Carl J. Koschmann"},{"1":"50","_rn_":"Peter J. Madsen"},{"1":"51","_rn_":"Jessica Wong"},{"1":"52","_rn_":"Anna R. Poetsch"},{"1":"53","_rn_":"Siyuan Zheng"},{"1":"54","_rn_":"Derek Hanson"},{"1":"55","_rn_":"Sharon J. Diskin"},{"1":"56","_rn_":"Laura Scolaro"},{"1":"57","_rn_":"Mariarita Santi"},{"1":"58","_rn_":"Miguel A. Brown"},{"1":"59","_rn_":"Adam C. Resnick"},{"1":"59","_rn_":"Meen Chul Kim"},{"1":"60","_rn_":"Casey S. Greene"},{"1":"61","_rn_":"Jo Lynne Rokita"},{"1":"62","_rn_":"Jaclyn N. Taroni"},{"1":"63","_rn_":"Children's Brain Tumor Network"},{"1":"64","_rn_":"Pacific Pediatric Neuro-Oncology Consortium"}],"options":{"columns":{"min":{},"max":[10]},"rows":{"min":[10],"max":[10]},"pages":{}}}
+{"columns":[{"label":[""],"name":["_rn_"],"type":[""],"align":["left"]},{"label":["all_contributors_positions"],"name":[1],"type":["dbl"],"align":["right"]}],"data":[{"1":"1","_rn_":"Joshua A. Shapiro"},{"1":"2","_rn_":"Krutika S. Gaonkar"},{"1":"3","_rn_":"Stephanie J. Spielman"},{"1":"4","_rn_":"Candace L. Savonen"},{"1":"5","_rn_":"Chante J. Bethell"},{"1":"6","_rn_":"Run Jin"},{"1":"7","_rn_":"Komal S. Rathi"},{"1":"8","_rn_":"Yuankun Zhu"},{"1":"9","_rn_":"Laura E. Egolf"},{"1":"10","_rn_":"Bailey K. Farrow"},{"1":"11","_rn_":"Daniel P. Miller"},{"1":"12","_rn_":"Yang Yang"},{"1":"13","_rn_":"Tejaswi Koganti"},{"1":"14","_rn_":"Nighat Noureen"},{"1":"15","_rn_":"Mateusz P. Koptyra"},{"1":"16","_rn_":"Nhat Duong"},{"1":"17","_rn_":"Mariarita Santi"},{"1":"18","_rn_":"Jung Kim"},{"1":"19","_rn_":"Shannon Robins"},{"1":"20","_rn_":"Phillip B. Storm"},{"1":"21","_rn_":"Stephen C. Mack"},{"1":"22","_rn_":"Jena V. Lilly"},{"1":"23","_rn_":"Hongbo M. Xie"},{"1":"24","_rn_":"Payal Jain"},{"1":"25","_rn_":"Pichai Raman"},{"1":"26","_rn_":"Brian R. Rood"},{"1":"27","_rn_":"Rishi R. Lulla"},{"1":"28","_rn_":"Javad Nazarian"},{"1":"29","_rn_":"Adam A. Kraya"},{"1":"30","_rn_":"Zalman Vaksman"},{"1":"31","_rn_":"Allison P. Heath"},{"1":"32","_rn_":"Cassie Kline"},{"1":"33","_rn_":"Laura Scolaro"},{"1":"34","_rn_":"Angela N. Viaene"},{"1":"35","_rn_":"Xiaoyan Huang"},{"1":"36","_rn_":"Gregory P. Way"},{"1":"37","_rn_":"Steven M. Foltz"},{"1":"38","_rn_":"Bo Zhang"},{"1":"39","_rn_":"Anna R. Poetsch"},{"1":"40","_rn_":"Sabine Mueller"},{"1":"41","_rn_":"Brian M. Ennis"},{"1":"42","_rn_":"Michael Prados"},{"1":"43","_rn_":"Sharon J. Diskin"},{"1":"44","_rn_":"Siyuan Zheng"},{"1":"45","_rn_":"Yiran Guo"},{"1":"46","_rn_":"Shrivats Kannan"},{"1":"47","_rn_":"Angela J. Waanders"},{"1":"48","_rn_":"Ashley S. Margol"},{"1":"49","_rn_":"Meen Chul Kim"},{"1":"50","_rn_":"Derek Hanson"},{"1":"51","_rn_":"Nicholas Van Kuren"},{"1":"52","_rn_":"Jessica Wong"},{"1":"53","_rn_":"Rebecca S. Kaufman"},{"1":"54","_rn_":"Noel Coleman"},{"1":"55","_rn_":"Christopher Blackden"},{"1":"56","_rn_":"Kristina A. Cole"},{"1":"57","_rn_":"Jennifer L. Mason"},{"1":"58","_rn_":"Peter J. Madsen"},{"1":"59","_rn_":"Carl J. Koschmann"},{"1":"60","_rn_":"Douglas R. Stewart"},{"1":"61","_rn_":"Eric Wafula"},{"1":"62","_rn_":"Miguel A. Brown"},{"1":"63","_rn_":"Adam C. Resnick"},{"1":"64","_rn_":"Casey S. Greene"},{"1":"65","_rn_":"Jo Lynne Rokita"},{"1":"66","_rn_":"Jaclyn N. Taroni"},{"1":"67","_rn_":"Children's Brain Tumor Network"},{"1":"68","_rn_":"Pacific Pediatric Neuro-Oncology Consortium"}],"options":{"columns":{"min":{},"max":[10]},"rows":{"min":[10],"max":[10]},"pages":{}}}
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analyses/count-contributions/results/module_contribution_counts.tsv

@@ -1,16 +1,16 @@
 author	num_modules
+Jo Lynne Rokita	28
 Krutika S. Gaonkar	27
 Jaclyn N. Taroni	26
-Jo Lynne Rokita	23
 Joshua A. Shapiro	21
 Candace L. Savonen	18
-Stephanie J. Spielman	15
+Stephanie J. Spielman	18
 Chante J. Bethell	11
 Run Jin	10
 Komal S. Rathi	6
 Laura E. Egolf	4
 Yuankun Zhu	4
-Bailey Farrow	3
+Bailey K. Farrow	3
 Daniel P. Miller	2
 Casey S. Greene	1
 Mateusz P. Koptyra	1

analyses/count-contributions/results/module_contributors.tsv

@@ -16,14 +16,16 @@ cnv-chrom-plot	Jaclyn N. Taroni
 cnv-chrom-plot	Joshua A. Shapiro
 cnv-chrom-plot	Jo Lynne Rokita
 cnv-chrom-plot	Stephanie J. Spielman
-collapse-rnaseq	Bailey Farrow
+collapse-rnaseq	Bailey K. Farrow
 collapse-rnaseq	Candace L. Savonen
 collapse-rnaseq	Jaclyn N. Taroni
 collapse-rnaseq	Joshua A. Shapiro
+collapse-rnaseq	Jo Lynne Rokita
 collapse-rnaseq	Komal S. Rathi
 collapse-rnaseq	Krutika S. Gaonkar
 collapse-rnaseq	Run Jin
 copy_number_consensus_call	Joshua A. Shapiro
+copy_number_consensus_call	Jo Lynne Rokita
 copy_number_consensus_call	Krutika S. Gaonkar
 copy_number_consensus_call	Nhat Duong
 focal-cn-file-preparation	Candace L. Savonen
@@ -63,9 +65,10 @@ immune-deconv	Komal S. Rathi
 immune-deconv	Stephanie J. Spielman
 independent-samples	Jaclyn N. Taroni
 independent-samples	Joshua A. Shapiro
+independent-samples	Jo Lynne Rokita
 independent-samples	Krutika S. Gaonkar
 independent-samples	Run Jin
-interaction-plots	Bailey Farrow
+interaction-plots	Bailey K. Farrow
 interaction-plots	Chante J. Bethell
 interaction-plots	Jaclyn N. Taroni
 interaction-plots	Joshua A. Shapiro
@@ -140,8 +143,10 @@ oncoprint-landscape	Run Jin
 oncoprint-landscape	Stephanie J. Spielman
 oncoprint-landscape	Yuankun Zhu
 run-gistic	Jaclyn N. Taroni
+run-gistic	Jo Lynne Rokita
 run-gistic	Krutika S. Gaonkar
 run-gistic	Run Jin
+run-gistic	Stephanie J. Spielman
 snv-callers	Candace L. Savonen
 snv-callers	Jaclyn N. Taroni
 snv-callers	Joshua A. Shapiro
@@ -155,9 +160,10 @@ survival-analysis	Jo Lynne Rokita
 survival-analysis	Krutika S. Gaonkar
 survival-analysis	Run Jin
 survival-analysis	Stephanie J. Spielman
-telomerase-activity-prediction	Bailey Farrow
+telomerase-activity-prediction	Bailey K. Farrow
 telomerase-activity-prediction	Candace L. Savonen
 telomerase-activity-prediction	Joshua A. Shapiro
+telomerase-activity-prediction	Jo Lynne Rokita
 telomerase-activity-prediction	Komal S. Rathi
 telomerase-activity-prediction	Nighat Noureen
 telomerase-activity-prediction	Stephanie J. Spielman
@@ -174,4 +180,6 @@ transcriptomic-dimension-reduction	Candace L. Savonen
 transcriptomic-dimension-reduction	Chante J. Bethell
 transcriptomic-dimension-reduction	Jaclyn N. Taroni
 transcriptomic-dimension-reduction	Krutika S. Gaonkar
+transcriptomic-dimension-reduction	Stephanie J. Spielman
 transcriptomic-dimension-reduction	Yuankun Zhu
+tumor-purity-exploration	Stephanie J. Spielman

analyses/count-contributions/results/total_contributions_clean.tsv

@@ -1,10 +1,10 @@
 author	num_commits
-Jaclyn N. Taroni	248
+Jaclyn N. Taroni	250
 Candace L. Savonen	149
+Stephanie J. Spielman	145
 Krutika S. Gaonkar	130
-Stephanie J. Spielman	118
+Jo Lynne Rokita	93
 Chante J. Bethell	88
-Jo Lynne Rokita	86
 Joshua A. Shapiro	53
 Casey S. Greene	35
 Yuankun Zhu	31
@@ -18,7 +18,7 @@ Tejaswi Koganti	5
 Ellen Kephardt	3
 Yang Yang	2
 Daniel P. Miller	2
-Bailey Farrow	1
+Bailey K. Farrow	1
 Mateusz P. Koptyra	1
 Pichai Raman	1
 Holly Beale	1