Issues

• Archive this repository

  AlexsLemonade/OpenPBTA-analysis#1760 · Filter by author jaclyn-taroni opened on Jun 19, 2023
  1

  

• MRAN will be retired July 1, 2023

  AlexsLemonade/OpenPBTA-analysis#1641 · Filter by author jaclyn-taroni opened on Jan 3, 2023

• Revision: Run and assess relevant survival models at threshold

  revisionwontfix
  AlexsLemonade/OpenPBTA-analysis#1627 · Filter by author sjspielman opened on Dec 12, 2022
  1

• Differences in mitochondrially-encoded gene expression between RNA-seq samples sequenced at BGI@CHOP vs. NantOmics

  data
  AlexsLemonade/OpenPBTA-analysis#1601 · Filter by author jaclyn-taroni opened on Aug 12, 2022
  1

• When MRAN is down, the build fails

  discussion
  AlexsLemonade/OpenPBTA-analysis#1250 · Filter by author sjspielman opened on Mar 21, 2022
  7

• CI can fail due to docker time outs

  cidiscussion
  AlexsLemonade/OpenPBTA-analysis#1225 · Filter by author sjspielman opened on Feb 16, 2022
  4

• Updated analysis: independent rna sample list selection

  bug
  AlexsLemonade/OpenPBTA-analysis#1103 · Filter by author kgaonkar6 opened on Jun 23, 2021
  5

• BS_WSFB4SA2 has BRAF p.V504_R506dup within kinase domain but not in hotspot INDEL file

  data
  AlexsLemonade/OpenPBTA-analysis#1058 · Filter by author jharenza opened on May 10, 2021

• Updated analysis: histology-treemap.html is broken -- probably delete it?

  updated analysis
  AlexsLemonade/OpenPBTA-analysis#920 · Filter by author cansavvy opened on Jan 22, 2021
  1

• Proposed Analysis: Batch effects in RNA-seq data

  proposed analysis
  AlexsLemonade/OpenPBTA-analysis#919 · Filter by author natemella opened on Jan 21, 2021
  14

• Question: Do we expect many participant IDs to be associated with more than one harmonized_diagnosis?

  dataquestion
  AlexsLemonade/OpenPBTA-analysis#913 · Filter by author jaclyn-taroni opened on Jan 16, 2021
  2

• Rerun analysis: comparative-RNASeq-analysis

  updated analysis
  AlexsLemonade/OpenPBTA-analysis#895 · Filter by author jashapiro opened on Jan 8, 2021
  6

  

• Updated analysis: Investigate handling of t-SNE in transcriptomic-dimension-reduction module

  updated analysis
  AlexsLemonade/OpenPBTA-analysis#716 · Filter by author cbethell opened on Jun 10, 2020
  5

• Discussion: Employ ENCODE blacklist to exclude problematic genomic regions

  cnvdiscussionupdated analysis
  AlexsLemonade/OpenPBTA-analysis#705 · Filter by author jashapiro opened on May 22, 2020
  1

• short_histology "Other" groups disparate types

  data
  AlexsLemonade/OpenPBTA-analysis#647 · Filter by author jashapiro opened on Mar 26, 2020
  3

• Use snakemake for pub-ready figure generation

  improvement
  AlexsLemonade/OpenPBTA-analysis#630 · Filter by author jaclyn-taroni opened on Mar 14, 2020
  6

• Proposed Analysis: GISTIC vs. focal-cn-file-preparation comparison

  proposed analysis
  AlexsLemonade/OpenPBTA-analysis#560 · Filter by author cbethell opened on Feb 26, 2020
  3

• Install MutSigCV on the project Docker image

  Docker-softwaresnv
  AlexsLemonade/OpenPBTA-analysis#546 · Filter by author jaclyn-taroni opened on Feb 19, 2020
  1

• Install FocalScan on the project Docker image

  cnvDocker-softwaretranscriptomic
  AlexsLemonade/OpenPBTA-analysis#545 · Filter by author jaclyn-taroni opened on Feb 19, 2020

• [Discussion] How should we define a recurrent mutation and how do our mutation results compare to the literature?

  discussionsnv
  AlexsLemonade/OpenPBTA-analysis#517 · Filter by author jaclyn-taroni opened on Feb 5, 2020
  3

• Updated analysis: "more nuanced" copy number calls

  cnvdiscussionimprovementupdated analysis
  AlexsLemonade/OpenPBTA-analysis#502 · Filter by author jaclyn-taroni opened on Feb 3, 2020

• Updated analysis: CNVkit consensus calls when tumor_ploidy > 2

  cnvdiscussionimprovementupdated analysis
  AlexsLemonade/OpenPBTA-analysis#501 · Filter by author jaclyn-taroni opened on Feb 3, 2020

• Updated analysis: rerun sex prediction from RNA-seq with v14 data

  transcriptomicupdated analysis
  AlexsLemonade/OpenPBTA-analysis#500 · Filter by author jaclyn-taroni opened on Feb 3, 2020
  1

• Discussion: possible improvements for copy number processing / analyses

  discussionimprovementupdated analysis
  AlexsLemonade/OpenPBTA-analysis#486 · Filter by author jaclyn-taroni opened on Jan 29, 2020

• Documentation: mapping between WGS/WXS RNA-seq pairs is confusing without documentation!

  documentation
  AlexsLemonade/OpenPBTA-analysis#399 · Filter by author jaclyn-taroni opened on Jan 3, 2020
  2