-
Hi Federico,
Thank you for this really nice and helpful package. It is really useful.
I used it for agronomical species (pig and bovine).
I encountered a problem when trying to use enhance_table…
-
perl vcf2maf.pl --input-vcf /path/to/somaticvariants.vcf --output-maf /path/to/out.maf --tumor-id s_MC7562_tumor --normal-id s_MC7562_germline --vep-path /path/to/vep/94/ --vep-data /path/to/vep91/cac…
-
Once sequence annotations is implemented, a search by feature ID for variant annotations should be added back in.
https://github.com/ga4gh/schemas/issues/577
-
From identifiers.org: UniProt:P04202 and https://identifiers.org/UniProt:P04202
In our go-cams: UniProtKB:P04202 and http://identifiers.org/uniprot/Q16629
[Example in Noctua-models](https://githu…
-
Hello,
I would like to run factR2 on a custom assembly where I ran in the issue described in [https://github.com/f-hamidlab/factR2/issues/7](issue#7). So I thought I try it on the example data you …
-
We noticed in the portal on the same protein location, we have different reference AAs.
Here is the link to all KIT samples in MSK portal. [**LINK**](https://cbioportal.mskcc.org/results/mutations?Ac…
-
From the gene.json file (https://data.bridgedb.org/gene.json), the following two .bridge files do not download:
- Ec_Derby_Ensembl_91.bridge
- Mx_Derby_Ensembl_85.bridge
Because of this, the Dock…
-
Hi,
When running NATMI (docker) on bulk data from mouse with Ensembel IDs the code broke, due to a duplicated entry in ids/10090_ensembl.csv.
The duplicated id is:
ENSMUSG00000115016,AA536875
…
-
In theory, Ensembl transcripts should not have gaps because they must align directly to a genome build. However, we know that there are examples of Ensembl transcripts even in GRCh38 where the alignme…
-
Hi,
I am running aracne.jar on my data set. But It is not generating output. First step: I calculated MI threshold. That was fine. After that, I used: java -Xmx5G -jar aracne.jar -e test/matrix.tx…