v1.0.0 - initial repo release

What's Changed

• Initial analysis and plot added to kinase_activity_corr module by @runjin326 in #2
• Revert "Initial analysis and plot added to kinase_activity_corr module" by @jharenza in #3
• ✨ added cwl for rmats by @dmiller15 in #5
• Kinase Activity Heatmap Added by @runjin326 in #4
• modified run module by @naqvia in #17
• Add docker file by @naqvia in #20
• move download script to root of repo by @jharenza in #21
• add packages for cluster analyses by @komalsrathi in #23
• Cluster analysis by @komalsrathi in #19
• create new data folder and download script by @jharenza in #28
• add issue and PR templates by @jharenza in #29
• add color palettes from OpenPBTA by @jharenza in #30
• updated dockerfile by @naqvia in #34
• general purpose theme by @naqvia in #36
• udpate packages by @naqvia in #35
• update dockerfile by @jharenza in #40
• updated docker by @naqvia in #41
• Sf regulation by @naqvia in #39
• Clk1 specific (1/N) by @naqvia in #25
• Expr vs splicing by @naqvia in #42
• Splicing index review by @naqvia in #31
• delete old/un-used code by @naqvia in #48
• delete files by @naqvia in #49
• update SI plot and rerun by @jharenza in #46
• splicing functional sites module review by @naqvia in #38
• added color palette tsv by @naqvia in #61
• updated docker file by @naqvia in #65
• Add heatmaps with annotations by @komalsrathi in #47
• script to compare splicing burden in high vs low CLK1 exon 4 groups by @naqvia in #64
• Expr vs splicing pr1 (2/N) new PR by @jharenza in #44
• venn diagram for diff SFs in clusters by @naqvia in #57
• add survival analyses by @rjcorb in #66
• Update survival analyses by @rjcorb in #71
• cluster members and splicing burden by @naqvia in #54
• Gsea analysis by @naqvia in #63
• Revert "Gsea analysis" by @naqvia in #74
• Create CODEOWNERS by @devbyaccident in #75
• updated to download gtf file and v3 by @naqvia in #68
• script to plot tmb of high vs low SBI tumors by @naqvia in #67
• added anaylsis to show histology make-up categorized by SBI level by @naqvia in #70
• cleaned up plot by @naqvia in #77
• v4 data download by @jharenza in #80
• Identify and plot histologies by sbi re run by @naqvia in #86
• added rmats comparison data file by @naqvia in #93
• fix typos by @naqvia in #89
• plot heatmap of CLK1 RNA vs SRSF phosp levels from CPTAC input data by @naqvia in #79
• Splicing events functional sites re-run by @naqvia in #94
• generate upsetR plot and table of histology specific splicing events by @naqvia in #84
• Revised gsea (re-done) by @naqvia in #76
• re-ran on new samples. no changes to code by @naqvia in #87
• Clustering module re run by @naqvia in #96
• Clk1 targets splicing by @naqvia in #108
• update dockerfile update by @naqvia in #121
• calculate and plot SBI by @naqvia in #113
• modified code to compute low vs high SBI within script by @naqvia in #85
• added v6 release by @naqvia in #123
• update v6 with new file by @naqvia in #125
• histology spec events plots by @naqvia in #115
• updated dockerfile by @naqvia in #127
• Add optimal clustering by @komalsrathi in #101
• CLK1 exon 4 impact on downstream gene expression (1/N) by @naqvia in #128
• CLK1 exon 4 impact on downstream gene expression (2/N) by @naqvia in #129
• Order heatmap rows by @komalsrathi in #131
• plots added by @naqvia in #135
• plot histologies across clusters by @naqvia in #132
• ORA of CLK1-mediated splice targets by @naqvia in #116
• cleaned up plots with colorblind-friendly colors by @naqvia in #78
• KNS42 DepMap analysis by @naqvia in #118
• Clk1 targets expr by @naqvia in #140
• Revert "Clk1 targets expr" by @naqvia in #156
• plot total splicing cases by @naqvia in #137
• update histology makeup per sbi level by @naqvia in #122
• fix colors to match color palette by @naqvia in #158
• increase size and dims of plots by @naqvia in #139
• Update Dockerfile by @naqvia in #168
• Update survival analyses with latest survival data and expanded HGG subtypes by @rjcorb in #166
• Circos plot by @naqvia in #163
• Re-generate SBI plots with plot groups (1/N) by @naqvia in #170
• Naqvia/170 re generate lollipop plots by @jharenza in #176
• code to plot distribution of SBI and ex 4 PSI (1/X) by @naqvia in #146
• updated upsetR plots by @naqvia in #174
• qpcr plot code (2/Y) by @naqvia in #164
• correlations of SRSF phosphoproteomic levels and CLK1 expression across brain tumors (3/X) by @naqvia in #148
• correlate CLK1 expr vs splicing (2/X) by @naqvia in #150
• Delete old cluster module + update histology barplot by cluster with new palette by @jharenza in #178
• modified heatmap code and uploaded raw cptac portal file (2/P) by @naqvia in #183
• cleaned up code and volcano plot for splicing factor module and also deleted old module folders (1/P) by @naqvia in #180
• Add required packages for optimal clustering by @komalsrathi in #185
• moved files to proper folders and updated readme by @naqvia in #199
• plot cell-proliferation results (1/Y) by @naqvia in #160
• added code to check TMB vs SBI by @naqvia in #202
• visualize long-RNA sequencing of CLK1 exon 4 by @naqvia in #144
• added code for high vs low sbi DE (2/N) by @naqvia in #203
• Update Dockerfile by @naqvia in #213
• update release- v7 by @naqvia in #218
• splicing events functional sites (1/K) by @naqvia in #208
• code to make CLK1 stacked plots (1/N) by @naqvia in #190
• fix mean line for stacked bar plots by @jharenza in #219
• Cohort summary module on v7 (1/X) by @naqvia in #222
• fix histologies bug - update release notes by @jharenza in #225
• Update release-notes.md for v14 pre-release histologies file by @jharenza in #226
• ran on latest histologies file by @naqvia in #227
• histology-specific splicing (2/X) by @naqvia in #221
• update SF-dysregulation module to compare HGGs of high vs low SBI by @naqvia in #216
• update splicing burden module by @naqvia in #228
• plot splice patterns code (2/K) by @naqvia in #209
• re-run functional sites module with modified perl code and v7 by @naqvia in #230
• re-run v7 on CLK1 correlations module by @naqvia in #231
• dockerfile update w package by @naqvia in #234
• v7 survival rerun by @jharenza in #233
• added code to subset for gene lists by @naqvia in #193
• modify sbi vs tmb plots by @naqvia in #242
• modify upsetR plots by @naqvia in #239
• update SF heatmap by @naqvia in #243
• change sbi barplot to percent, change dims by @jharenza in #244
• modify func plot by @naqvia in #254
• Updated qPCR plot: fix housekeeping gene calculations by @jharenza in #253
• modified plot and fixed deseq table by @naqvia in #255
• changed Fig2D volc plot aesthetics by @naqvia in #256
• report kinases and frequency + site + preference (1/Z) by @naqvia in #246
• (1/A) - run GSVA on CLK1 treated cell lines by @jharenza in #257
• Rerun clustering on v7 data by @naqvia in #184
• plot upload by @naqvia in #262
• factor high/low SBI for volcano by @jharenza in #263
• suppl tables (2/Z) by @naqvia in #245
• added scripts for functional sites - (1/P) by @naqvia in #260
• Update ORA on DS (2/P) by @naqvia in #261
• (3/P) GSVA comparisons and plots by @jharenza in #258
• aesthetic updates to cluster pathway heatmap and reduce n to 5 by @jharenza in #266
• update circos plot to say "Gender" instead of sex by @jharenza in #275
• Add corplots for TMB vs SBI for supplemental figures by @jharenza in #276
• add gg venn to docker by @naqvia in #272
• intersect DES and DEX by @naqvia in #264
• rm old CLK1 module by @naqvia in #281
• Mean CLK1 PSI - write out ti file by @jharenza in #285
• Updates to correlation plots/ heatmaps by @jharenza in #280
• fix y-axis for cor plots by @jharenza in #288
• added optimal clustering output by @naqvia in #268
• added subtypes suppl. plot code by @naqvia in #273
• update sbi/tmb plots with new tmb file (2/2) by @jharenza in #292
• Update clustering README by @komalsrathi in #291
• oncoprint (1/2) by @naqvia in #210
• added table for functional sites (morpho-treated vs untreated) by @naqvia in #293
• add CLK1 to goi list for oncoprint by @jharenza in #301
• modified code to change plot by @naqvia in #295
• separate clk1 high low vs sbi by HGG plot groups by @jharenza in #302
• subtype specific CLK1 Exon 4 PSI plots by @naqvia in #304
• added primers table by @naqvia in #297
• Asses HGG survival by CLK1 status by @rjcorb in #298
• subsetted for CLK1 in rmats tsv by @naqvia in #313
• add v8 data release by @jharenza in #312
• added code to make lolliplot of total splicing cases by @naqvia in #308
• use tpm correlations clk1 psi by @naqvia in #317
• Assess correlation between CLK1 features and CLK, SRSF RNA, protein and phosphoprotein expression by @rjcorb in #307
• V8 release by @jharenza in #314
• Plot CLK1 exon 4 expression in HGGs, GTEX, and pediatric normal brains (2/2) by @jharenza in #315
• polyA vs stranded PSI by @naqvia in #303
• Fig 3B by @naqvia in #311
• Cluster pathways heatmap - update to hallmark, reduce N by @jharenza in #320
• update dockerfile to R4.4 and BioC 3.19 by @jharenza in #322
• high vs low diff. expr by hgg subtypes by @naqvia in #305
• CLK1 Exon 4 impact on NF1 splicing by @naqvia in #318
• add hmisc package to Docker by @naqvia in #327
• Add NF1 protein correlations by @jharenza in #329
• updated docker with gvsa by @naqvia in #334
• Updates cluster geneset pathways and GSVA code by @jharenza in #333
• Correlate SBI vs GSVA score by @naqvia in #339
• Update corplot visuals for manuscript (1/N) by @jharenza in #330
• Add fusions, NF1 splicing and protein to oncoprint (2/2) by @jharenza in #331
• tmb log10 scatter plots against SBI by @naqvia in #340
• export diff splice events tsv file by @naqvia in #337
• Update survival forest plot CIs by @rjcorb in #341
• fix figure5d typo by @jharenza in #352
• cell proliferation plot for CLK1-inhibitor by @naqvia in #350
• Update splicing factor dysregulation protein heatmap by @jharenza in #354
• functional sites for non-SE cases by @naqvia in #347
• add cluster, nf1 psi survival analyses by @rjcorb in #343
• prioritize HOPE proteomics over CPTAC by @rjcorb in #360
• venn diagram updates by @naqvia in #357
• update docker by @naqvia in #359
• Rokita/update morph gsva - required per R 4.4 /GSVA package update by @jharenza in #342
• update SI plot colors by @jharenza in #365
• Add all samples to clk1/nf1 rna/protein file (1/2) by @jharenza in #345
• Rerun CLK1 PSI survival (2/2) by @rjcorb in #346
• fix kinase output by @naqvia in #367
• update onco/tsg anno (1/2) by @jharenza in #369
• rerun tables (2/2) by @jharenza in #370
• v9 release - update to tumor only maf by @jharenza in #378
• update gender colors in cohort summary plot by @jharenza in #381
• v9 release modification: freec wxs to consensus (1/2) by @jharenza in #380
• make clean oncoprint branch, adding SF oncoprint (2/2) by @jharenza in #379
• CTG plot update by @naqvia in #384
• added SFs to suppl tables by @naqvia in #385
• rm tgen samples from gtex plot by @jharenza in #387
• prioritize hope in script 06, add NF1-201 to cor plots and heatmaps by @jharenza in #389
• subset 10 DMGs before zscoring for single sample heatmap by @jharenza in #392
• fix labeling on plots, add cor by @jharenza in #391
• rm nf1 tracks from oncoprint by @jharenza in #395
• CRISPR intersection with CLK1 targets by @naqvia in #393
• added tab to S5 by @naqvia in #396
• update-dockerfile by @jharenza in #397
• using oncokb by @naqvia in #399
• change recurrent cut-off to 17%/histology by @naqvia in #401
• Rokita/table rerun by @jharenza in #407
• update dims SBI plot by @jharenza in #402
• update colors of kinase plot per priyanka feedback by @jharenza in #404
• run script by @naqvia in #388
• readme updates by @naqvia in #408
• Update title by @jharenza in #410

New Contributors

• @runjin326 made their first contribution in #2
• @dmiller15 made their first contribution in #5
• @devbyaccident made their first contribution in #75

Full Changelog: https://github.com/d3b-center/pbta-splicing/commits/v1.0.0