d3b-center/hope-cohort-analysis

Issues

• Modify README file to update analysis modules list and descriptions

  #75 opened a month ago by JosephDybas
  4

• Move Pleomorphic xanthoastrocytoma into cancer_group_short HGG

  #86 opened a month ago by jharenza
  1

• Add two samples' genomic data back to HOPE cohort

  #104 opened a month ago by jharenza
  3

• Create oncoprint using Sinai mutation data

  #119 opened a month ago by komalsrathi
  0

• Update dockerfile to use R 4.4/BioC 3.19

  #103 opened 5 months ago by jharenza
  0

• Update manuscript plots

  #101 opened 8 months ago by komalsrathi
  0

• Update circlize package to >= 0.4.14

  #99 opened 9 months ago by jharenza
  1

• Update: ALT Analysis

  #87 opened 9 months ago by komalsrathi
  5

• Add PXA and Cancer_Group (Expanded abbreviation) column to annotation file

  #95 opened 10 months ago by jharenza
  2

• Update: Cascade Plots (All genes)

  #90 opened 10 months ago by komalsrathi
  0

• Update: Cascade Plots (Top 20 genes)

  #89 opened 10 months ago by komalsrathi
  0

• Update: Data availability circos plot

  #88 opened 10 months ago by komalsrathi
  6

• October 2023 figures updates

  #77 opened a year ago by mkoptyra
  31

• Re-run analyses

  #52 opened a year ago by komalsrathi
  0

• Harmonize HOPE_diagnosis_type in histologies file

  #78 opened a year ago by komalsrathi
  1

• Add workflow of how molecular subtype has been done

  #74 opened a year ago by zzgeng
  1

• Proteomic-data module update

  #59 opened a year ago by zzgeng
  3

• Update Docker files

  #82 opened a year ago by zzgeng
  1

• Liftover the gene symbol for Proteomic/Phospho data

  #43 opened a year ago by zzgeng
  1

• V2 data release

  #63 opened a year ago by zzgeng
  2

• Add proteomics matrices

  #40 opened a year ago by jharenza
  1

• Packages missing from dockerfile

  #37 opened a year ago by jharenza
  1

• remove files from scratch, add gitignore

  #46 opened a year ago by jharenza
  1

• Regenerate files with new base histology file

  #49 opened a year ago by zzgeng
  3

• add PXA BRAF V600E to subtyping

  #27 opened a year ago by jharenza
  1

• Organize directories and code

  #28 opened a year ago by komalsrathi
  0

• README for all modules

  #30 opened a year ago by komalsrathi
  0

• Filter fusion files based on the gene expression

  #26 opened a year ago by zzgeng
  2

• New merge files for s3 v1 folder

  #35 opened a year ago by jharenza
  9

• Re-merge MAF files

  #31 opened a year ago by jharenza
  15

• Finalizing figures for version 1 manuscript Hope cohort

  #13 opened a year ago by mkoptyra
  10

• add data download script for repo

  #15 opened a year ago by jharenza
  1

• Add merged files and md5sum.txt to s3 bucket

  #14 opened a year ago by jharenza
  12

• create dockerfile

  #16 opened a year ago by jharenza
  1

• Update `Hope-fusion-putative-oncogenic.rds`

  #22 opened a year ago by jharenza
  1

• Additional requests from Mateusz

  #12 opened 2 years ago by komalsrathi
  0

• Create cascade plots

  #11 opened 2 years ago by komalsrathi
  0

• ALT status correlation with clinical variables

  #10 opened 2 years ago by komalsrathi
  0

• TMB calculation

  #9 opened 2 years ago by komalsrathi
  1

• Correlation of microsatellite instability and proteomics cluster assignment

  #8 opened 2 years ago by komalsrathi
  0

• Mutational landscape of Hope cohort based on the age hierarchy

  #5 opened 3 years ago by mkoptyra
  7

• Correlation of gene alterations vs clinical variables

  #7 opened 3 years ago by komalsrathi
  2

• Circos plot on tissue annotation for the Hope cohort

  #6 opened 3 years ago by mkoptyra
  1

• Update oncoprints

  #4 opened 3 years ago by komalsrathi
  0

• Update data

  #3 opened 3 years ago by komalsrathi
  0

• Oncoprint order

  #2 opened 3 years ago by komalsrathi
  0

• Analysis request: HOPE cohort Oncoplot

  #1 opened 3 years ago by komalsrathi
  2