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broadinstitute
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depmap_omics
What you need to process the Quarterly DepMap-Omics releases from Terra
https://depmap.org/portal/
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Move guide mutation matrix generation to wdl
#190
5im1z
closed
8 months ago
1
Aggregation of microsatellite repeats per site per cell line
#189
iboyle-broad
closed
9 months ago
0
don't let purecn failures overwrite wgs seg count qc failures
#188
5im1z
closed
8 months ago
0
debug: cn postprocessing function blists wrong seq entries
#187
5im1z
closed
8 months ago
0
move TERT mutation rescue from postprocessing to vcf_to_depmap
#186
5im1z
closed
8 months ago
0
Add tert rescue to wdl (instead of bq in postprocessing)
#185
5im1z
closed
8 months ago
0
Add wgs cram qc
#184
5im1z
closed
8 months ago
1
Rescue masked genecn
#183
5im1z
closed
9 months ago
1
germline tag bugfix for fix_mutect2
#182
gulatide
closed
7 months ago
3
add jupyter notebook for chrM renormalization of RNA-seq
#181
qinqian
closed
9 months ago
0
Add hotspot column to maf
#180
5im1z
closed
9 months ago
0
add hotspot as a column in mutation table
#179
5im1z
closed
9 months ago
0
use mutation rescue list to un-mask cn genes
#178
5im1z
closed
9 months ago
0
Bump aiohttp from 3.8.4 to 3.8.6
#177
dependabot[bot]
closed
8 months ago
1
Bump pyarrow from 11.0.0 to 14.0.1
#176
dependabot[bot]
closed
8 months ago
1
creating mutation matrices too slow
#175
qinqian
closed
8 months ago
0
Convert the WGS_CCLE jupyter notebook into command line in the future
#174
qinqian
opened
1 year ago
0
Bump urllib3 from 1.26.14 to 1.26.18
#173
dependabot[bot]
closed
8 months ago
1
finalize mutation post processing
#172
5im1z
closed
1 year ago
2
Bump pillow from 9.4.0 to 10.0.1
#171
dependabot[bot]
closed
8 months ago
1
Bump urllib3 from 1.26.14 to 1.26.17
#170
dependabot[bot]
closed
1 year ago
1
Update vcf to depmap
#169
5im1z
closed
1 year ago
0
correct indel pos
#168
qinqian
closed
1 year ago
1
Duplicate RNA-seq omics profiles for cell lines
#167
mjsteinbaugh
closed
1 year ago
2
refactor vcf_to_depmap that is compatible with latest MAF format
#166
qinqian
closed
1 year ago
2
Availability of PureCN copy number calls for DepMap 23Q2
#165
ssrinivasan2
closed
1 year ago
1
Reference files for PureCN pipeline
#164
miachom
closed
1 year ago
8
Merge annotators: qc filter - mask repeats - hgvs - opencravat
#163
5im1z
closed
1 year ago
0
Bump jupyter-server from 2.4.0 to 2.7.2
#162
dependabot[bot]
closed
8 months ago
1
add quality filter and segdup/rm masking to merged mutation pipeline
#161
5im1z
closed
1 year ago
0
mask segmental duplication and repeat masker regions
#160
5im1z
closed
1 year ago
0
Mask repeats and segdups
#159
5im1z
closed
1 year ago
0
New cell lines in 23q2 release not at Cellosaurus (no RRID)
#158
mjsteinbaugh
closed
1 year ago
1
Devel telomere
#157
qinqian
closed
1 year ago
0
Add effective length
#156
5im1z
closed
1 year ago
0
Generate RNAseq effective length matrix
#155
5im1z
closed
1 year ago
0
hgvs: make machine params part of workflow input
#154
5im1z
closed
1 year ago
1
Add aneuploidy
#153
5im1z
closed
1 year ago
0
Fixes for loading bigquery from parquet tables
#152
pgm
closed
1 year ago
0
Arm-level CNA and aneuploidy score
#151
5im1z
closed
1 year ago
0
Update vcf to depmap
#150
5im1z
closed
1 year ago
0
Dev hgvs
#149
qinqian
closed
1 year ago
0
Add oncokb to oc
#148
5im1z
closed
1 year ago
0
Qq vcf2maf test
#147
qinqian
closed
1 year ago
0
Bump certifi from 2022.12.7 to 2023.7.22
#146
dependabot[bot]
closed
1 year ago
2
Bump pygments from 2.14.0 to 2.15.0
#145
dependabot[bot]
closed
1 year ago
2
Bump aiohttp from 3.8.4 to 3.8.5
#144
dependabot[bot]
closed
1 year ago
2
Pgm sample test
#143
qinqian
closed
1 year ago
1
Add cosmic to oc
#142
5im1z
closed
1 year ago
0
add cosmic actionability annotation to open cravat
#141
5im1z
closed
1 year ago
0
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