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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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update imported WDL gists
#234
dpmccabe
opened
2 days ago
0
Small changes to hermit dockerfile and script
#233
pgm
closed
2 days ago
0
add latest batch correction notebook
#232
qinqian
opened
3 days ago
0
SV matrix needs index
#231
5im1z
closed
4 days ago
0
Update rna pipeline for crams
#230
5im1z
closed
4 days ago
0
Add rescue reason to maf
#229
5im1z
closed
4 days ago
0
SSDs not HDDs
#228
dpmccabe
closed
1 week ago
0
Add Intron and Exon columns to maf, rescue MET intron13 mutations
#227
5im1z
closed
6 days ago
1
Add microsatellite repeats to postprocessing
#226
5im1z
closed
2 weeks ago
0
SV postprocessing debug
#225
5im1z
closed
1 week ago
0
SV debug: corrected input name to vep
#224
5im1z
closed
2 weeks ago
0
actually pass major contig bool to the task
#223
5im1z
closed
2 weeks ago
0
updated SV workflow in WGS_pipeline
#222
5im1z
closed
2 weeks ago
0
Annotation used for DepMap 24Q2 release
#221
fgypas
opened
3 weeks ago
1
Cn geneid remap
#220
5im1z
closed
4 days ago
0
Vep sv
#219
5im1z
closed
3 weeks ago
1
Vep sv
#218
5im1z
closed
1 month ago
0
made a change so that my dev branch should be added to the vcf_to_depmap wdl
#217
GoldenLA
closed
2 months ago
0
changed dockstore yml
#216
GoldenLA
closed
2 months ago
0
upload stranded transcripts and all gene matrices to postprocessing
#215
5im1z
closed
4 days ago
0
Bump urllib3 from 1.26.14 to 1.26.19
#214
dependabot[bot]
closed
2 months ago
1
remove noop commands from annotate_hgvs_task
#213
dpmccabe
closed
1 month ago
0
drop wes SV from postprocessing
#212
5im1z
closed
2 months ago
0
Bump tornado from 6.2 to 6.4.1
#211
dependabot[bot]
closed
2 months ago
1
Bump requests from 2.28.2 to 2.32.0
#210
dependabot[bot]
closed
2 months ago
1
Bump jinja2 from 3.1.2 to 3.1.4
#209
dependabot[bot]
closed
2 months ago
1
Bump tqdm from 4.65.0 to 4.66.3
#208
dependabot[bot]
closed
2 months ago
1
Bump pydantic from 1.10.5 to 1.10.13
#207
dependabot[bot]
closed
2 months ago
1
Bump aiohttp from 3.8.4 to 3.9.4
#206
dependabot[bot]
closed
2 months ago
1
Bump idna from 3.4 to 3.7
#205
dependabot[bot]
closed
2 months ago
1
Rework rnastrand wdl
#204
5im1z
closed
3 days ago
1
Bump pillow from 9.4.0 to 10.3.0
#203
dependabot[bot]
closed
2 months ago
1
remove async and await
#202
5im1z
closed
5 months ago
1
remove log transform for relative cn
#201
5im1z
closed
5 months ago
2
manually classify 2 TERT promoter mutations as hotspots
#200
5im1z
closed
5 months ago
0
Add splice ai annotation to maf
#199
5im1z
closed
5 months ago
0
Dragen preprocess fix
#198
5im1z
closed
5 months ago
0
Add strandedness to postprocessing
#197
5im1z
closed
5 months ago
0
Are we able to download latest data showed in website from this site?
#196
AR-Shicheng
closed
5 months ago
1
new oncokb data table that has braf v600e (and many others!)
#195
5im1z
closed
5 months ago
1
Add rnaseqc2 counts to post
#194
5im1z
closed
5 months ago
2
Rna strandness fix
#193
qinqian
closed
3 days ago
1
Rna renormalize
#192
qinqian
closed
3 days ago
1
add alpha missense
#191
5im1z
closed
6 months ago
0
Move guide mutation matrix generation to wdl
#190
5im1z
closed
7 months ago
1
Aggregation of microsatellite repeats per site per cell line
#189
iboyle-broad
closed
7 months ago
0
don't let purecn failures overwrite wgs seg count qc failures
#188
5im1z
closed
7 months ago
0
debug: cn postprocessing function blists wrong seq entries
#187
5im1z
closed
7 months ago
0
move TERT mutation rescue from postprocessing to vcf_to_depmap
#186
5im1z
closed
7 months ago
0
Add tert rescue to wdl (instead of bq in postprocessing)
#185
5im1z
closed
7 months ago
0
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