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 #2...