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For the purposes of debugging etc, and to allow referencing a specific release, I think we should add some versioning of the portal to the idc-dev and idc-testing pages. Thoughts?
@wlongabaugh @G-W…
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There are many studies with `NA` in either REFERENCE_ALLELE or TUMOR_SEQ_ALLELE
Our annotator seems to be able to handle NA in REFERENCE_ALLELE but not in TUMOR_SEQ_ALLELE
![image](https://user-im…
jjgao updated
3 years ago
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# Requester information
Please provide the following information:
Name: Eric Torstenson
Affiliation: VUMC (Vanderbilt)
# Request Details
Please provide the following information about what you …
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See issue described in https://discourse.canceridc.dev/t/understanding-idc-portal-cohort-plots/81.
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JB2 port of Andrew Duncan's (@agduncan94) JB1 plugin that browses and imports GDC data.
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##### Issue Type
- Bug Report
##### Summary
Migrating GoCD from 20.4 to 20.7 business continuity does not work as expected
##### Environment
Full logs is to big to be submitted here, plea…
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In the public portal database, there are a few different values for `NCBI_BUILD`. But we should only have one version (GRCh37/hg19) in our database. Let's:
- [x] change hg19 to GRCh37 (either in th…
jjgao updated
4 years ago
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I would like to use the ScanNeo pipeline and would like to reproduce the results described in the [paper](https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btz193/5384…
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I just started to use R maftools. It is a great package, however there seems to be a bug when reading gzipped maf.
For example, using this public file from TCGA https://portal.gdc.cancer.gov/files/9…
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On the exploration tab of the GDC portal, I can identify 71 TCGA samples which are solid tissue normal samples from ovarian tissue:
![image](https://user-images.githubusercontent.com/976675/7396650…