d3b-center/hope-cohort-analysis: Initial manuscript submission

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