Comments (1)
Hi Shicheng,
Please refer to the latest comment in this thread in our public forum. Let me know if that answers your question.
Thanks,
Simone
from depmap_omics.
Related Issues (20)
- add timestamped CIVIC db
- update mutation mapping to entrez
- automate STR inference + gumbo import in fingerprinting
- add cosmic actionability annotation to open cravat
- Arm-level CNA and aneuploidy score
- Generate RNAseq effective length matrix
- New cell lines in 23q2 release not at Cellosaurus (no RRID) HOT 1
- mask segmental duplication and repeat masker regions
- add quality filter and segdup/rm masking to merged mutation pipeline
- Reference files for PureCN pipeline HOT 8
- Availability of PureCN copy number calls for DepMap 23Q2 HOT 1
- refactor vcf_to_depmap that is compatible with latest MAF format HOT 2
- Duplicate RNA-seq omics profiles for cell lines HOT 2
- Convert the WGS_CCLE jupyter notebook into command line in the future
- creating mutation matrices too slow
- use mutation rescue list to un-mask cn genes
- add hotspot as a column in mutation table
- move TERT mutation rescue from postprocessing to vcf_to_depmap
- debug: cn postprocessing function blists wrong seq entries
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from depmap_omics.