What's Changed Annotate fusions by @komalsrathi in https://github.com/d3b-center/hope-cohort-analysis/pull/23 Add Dockerfile by @zzgeng in https://github.com/d3b-center/hope-cohort-analysis/pull/18 Add download script (1/N) by @zzgeng in https://github.com/d3b-center/hope-cohort-analysis/pull/17 Change the download directory for gencode 39 by @zzgeng in https://github.com/d3b-center/hope-cohort-analysis/pull/32 Organize code by @komalsrathi in https://github.com/d3b-center/hope-cohort-analysis/pull/29 Add pathology based on molecular subtyping results (5/N) by @zzgeng in https://github.com/d3b-center/hope-cohort-analysis/pull/34 Add script to subset files for molecular subtyping (3/N) by @zzgeng in https://github.com/d3b-center/hope-cohort-analysis/pull/24 Add tp53 score module (2/N) by @zzgeng in https://github.com/d3b-center/hope-cohort-analysis/pull/20 Add release note by @zzgeng in https://github.com/d3b-center/hope-cohort-analysis/pull/36 fwrite tab delimited by @komalsrathi in https://github.com/d3b-center/hope-cohort-analysis/pull/44 Add gitignore and remove files in scratch by @zzgeng in https://github.com/d3b-center/hope-cohort-analysis/pull/48 Update in tp53 score module: change the script to use both cnv files as input (1/2) by @zzgeng in https://github.com/d3b-center/hope-cohort-analysis/pull/45 Update in molecular_subtyping module: change the script to use both cnv files as input (2/2) by @zzgeng in https://github.com/d3b-center/hope-cohort-analysis/pull/47 Use histology file to filter samples by @komalsrathi in https://github.com/d3b-center/hope-cohort-analysis/pull/50 Update docker file to add missing packages by @zzgeng in https://github.com/d3b-center/hope-cohort-analysis/pull/38 Fix tp53 script CNV issue by @zzgeng in https://github.com/d3b-center/hope-cohort-analysis/pull/51 Add CPTAC sample tp53 score by @zzgeng in https://github.com/d3b-center/hope-cohort-analysis/pull/53 Update 4844 subtyping by @jharenza in https://github.com/d3b-center/hope-cohort-analysis/pull/54 Add BS_id to proteomic data by @zzgeng in https://github.com/d3b-center/hope-cohort-analysis/pull/41 Add new integrated dx from pathology review by @jharenza in https://github.com/d3b-center/hope-cohort-analysis/pull/55 generate telomere ratio by @jharenza in https://github.com/d3b-center/hope-cohort-analysis/pull/67 Add sample_id column in combined_score.tsv by @zzgeng in https://github.com/d3b-center/hope-cohort-analysis/pull/66 Add K28I mutation in HGG mutation by @zzgeng in https://github.com/d3b-center/hope-cohort-analysis/pull/64 Add CPTAC GBM TP53 mutations by @jharenza in https://github.com/d3b-center/hope-cohort-analysis/pull/68 restore snv counts for AYA by @jharenza in https://github.com/d3b-center/hope-cohort-analysis/pull/69 Survival analysis for HOPE cohort (2/2) by @zzgeng in https://github.com/d3b-center/hope-cohort-analysis/pull/57 Add summary stats plot for tp53 score (1/2) by @zzgeng in https://github.com/d3b-center/hope-cohort-analysis/pull/56 revert sample removal - not subtyped anyway by @jharenza in https://github.com/d3b-center/hope-cohort-analysis/pull/72 Add readme to molecular-subtyping-HGG module by @zzgeng in https://github.com/d3b-center/hope-cohort-analysis/pull/71 Add readme to proteomic-data (1/N) by @zzgeng in https://github.com/d3b-center/hope-cohort-analysis/pull/61 Update README.md by @jharenza in https://github.com/d3b-center/hope-cohort-analysis/pull/58 add binned age for 16-40, 2 group AYA by @jharenza in https://github.com/d3b-center/hope-cohort-analysis/pull/73 Add ggalluvial package to dockerfile by @zzgeng in https://github.com/d3b-center/hope-cohort-analysis/pull/83 Add predicted ancestry to TP53 score summary plot by @zzgeng in https://github.com/d3b-center/hope-cohort-analysis/pull/76 Change the label of alluvial plot by @zzgeng in https://github.com/d3b-center/hope-cohort-analysis/pull/85 V2 histology file: Add cancer_group_short column in final histology file by @zzgeng in https://github.com/d3b-center/hope-cohort-analysis/pull/65 V2 release: Update download script for v2 by @zzgeng in https://github.com/d3b-center/hope-cohort-analysis/pull/70 Add workflow to HGG molecular subtyping by @zzgeng in https://github.com/d3b-center/hope-cohort-analysis/pull/81 Reform proteomic output data (2/N) by @zzgeng in https://github.com/d3b-center/hope-cohort-analysis/pull/62 Rerun analyses by @komalsrathi in https://github.com/d3b-center/hope-cohort-analysis/pull/80 Update README.md by @JosephDybas in https://github.com/d3b-center/hope-cohort-analysis/pull/91 Update README.md by @JosephDybas in https://github.com/d3b-center/hope-cohort-analysis/pull/92 Update age continuous color by @komalsrathi in https://github.com/d3b-center/hope-cohort-analysis/pull/94 Update cascade plots by @komalsrathi in https://github.com/d3b-center/hope-cohort-analysis/pull/93 GSVA analysis of proteomics data by @JosephDybas in https://github.com/d3b-center/hope-cohort-analysis/pull/79 Update annotation file by @komalsrathi in https://github.com/d3b-center/hope-cohort-analysis/pull/96 Annotation file for data availability plot by @komalsrathi in https://github.com/d3b-center/hope-cohort-analysis/pull/97 Add master annotation by @komalsrathi in https://github.com/d3b-center/hope-cohort-analysis/pull/98 Dockerfile update by @jharenza in https://github.com/d3b-center/hope-cohort-analysis/pull/100 Remove 7316-3625 from manuscript plots/master annotation file by @komalsrathi in https://github.com/d3b-center/hope-cohort-analysis/pull/102 Update order of analyses (1/11) by @komalsrathi in https://github.com/d3b-center/hope-cohort-analysis/pull/113 update dockerfile to R4.4, reorg by @jharenza in https://github.com/d3b-center/hope-cohort-analysis/pull/107 Update merge files code (2/11) by @komalsrathi in https://github.com/d3b-center/hope-cohort-analysis/pull/105 add txdbmaker by @komalsrathi in https://github.com/d3b-center/hope-cohort-analysis/pull/118 Update tp53_nf1_score module (3/11) by @komalsrathi in https://github.com/d3b-center/hope-cohort-analysis/pull/106 Update README.md by @jharenza in https://github.com/d3b-center/hope-cohort-analysis/pull/123 New Contributors @jharenza made their first contribution in https://github.com/d3b-center/hope-cohort-analysis/pull/54 @JosephDybas made their first contribution in https://github.com/d3b-center/hope-cohort-analysis/pull/91 Full Changelog: https://github.com/d3b-center/hope-cohort-analysis/commits/v1.0.0