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This repository has been archived by the owner on Jun 21, 2023. It is now read-only.

Issues: AlexsLemonade/OpenPBTA-analysis

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Issues list

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#1760 opened Jun 19, 2023 by jaclyn-taroni
@jaclyn-taroni
1
MRAN will be retired July 1, 2023
#1641 opened Jan 3, 2023 by jaclyn-taroni
Revision: Run and assess relevant survival models at threshold revision Related to manuscript revisions wontfix This will not be worked on
#1627 opened Dec 12, 2022 by sjspielman
1
Differences in mitochondrially-encoded gene expression between RNA-seq samples sequenced at BGI@CHOP vs. NantOmics data
#1601 opened Aug 12, 2022 by jaclyn-taroni
1
When MRAN is down, the build fails discussion
#1250 opened Mar 21, 2022 by sjspielman
7
CI can fail due to docker time outs ci Related to continuous integration discussion
#1225 opened Feb 16, 2022 by sjspielman
4
Updated analysis: independent rna sample list selection bug Something isn't working
#1103 opened Jun 23, 2021 by kgaonkar6
5
BS_WSFB4SA2 has BRAF p.V504_R506dup within kinase domain but not in hotspot INDEL file data
#1058 opened May 10, 2021 by jharenza
Updated analysis: histology-treemap.html is broken -- probably delete it? updated analysis
#920 opened Jan 22, 2021 by cansavvy
1
Proposed Analysis: Batch effects in RNA-seq data proposed analysis
#919 opened Jan 21, 2021 by natemella
14
Question: Do we expect many participant IDs to be associated with more than one harmonized_diagnosis? data question Further information is requested
#913 opened Jan 16, 2021 by jaclyn-taroni
2
Rerun analysis: comparative-RNASeq-analysis updated analysis
#895 opened Jan 8, 2021 by jashapiro
@cansavvy
6
Updated analysis: Investigate handling of t-SNE in transcriptomic-dimension-reduction module updated analysis
#716 opened Jun 10, 2020 by cbethell
5
Discussion: Employ ENCODE blacklist to exclude problematic genomic regions cnv Related to or requires CNV data discussion updated analysis
#705 opened May 22, 2020 by jashapiro
1
short_histology "Other" groups disparate types data
#647 opened Mar 26, 2020 by jashapiro
3
Use snakemake for pub-ready figure generation improvement
#630 opened Mar 14, 2020 by jaclyn-taroni
6
Proposed Analysis: GISTIC vs. focal-cn-file-preparation comparison proposed analysis
#560 opened Feb 26, 2020 by cbethell
3
Install MutSigCV on the project Docker image Docker-software Use this label for help getting certain software into the docker container snv Related to or requires SNV data
#546 opened Feb 19, 2020 by jaclyn-taroni
1
Install FocalScan on the project Docker image cnv Related to or requires CNV data Docker-software Use this label for help getting certain software into the docker container transcriptomic Related to or requires transcriptomic data
#545 opened Feb 19, 2020 by jaclyn-taroni
[Discussion] How should we define a recurrent mutation and how do our mutation results compare to the literature? discussion snv Related to or requires SNV data
#517 opened Feb 5, 2020 by jaclyn-taroni
3
Updated analysis: "more nuanced" copy number calls cnv Related to or requires CNV data discussion improvement updated analysis
#502 opened Feb 3, 2020 by jaclyn-taroni
Updated analysis: CNVkit consensus calls when tumor_ploidy > 2 cnv Related to or requires CNV data discussion improvement updated analysis
#501 opened Feb 3, 2020 by jaclyn-taroni
Updated analysis: rerun sex prediction from RNA-seq with v14 data transcriptomic Related to or requires transcriptomic data updated analysis
#500 opened Feb 3, 2020 by jaclyn-taroni
1
Discussion: possible improvements for copy number processing / analyses discussion improvement updated analysis
#486 opened Jan 29, 2020 by jaclyn-taroni
Documentation: mapping between WGS/WXS RNA-seq pairs is confusing without documentation! documentation Improvements or additions to documentation
#399 opened Jan 3, 2020 by jaclyn-taroni
2
ProTip! Follow long discussions with comments:>50.