-
Hello,
I am trying to annotate a VCF file and I am getting this error:
dotnet /home/gtc-bioit/Downloads/Nirvana-v3.18.1/Nirvana.dll -i test.vcf --out /mnt/Reports/BaseSpace/PanCancer/2022/2022-0
…
-
Although it does not cause a failure, duplicated key in YAML should probably be avoid:
https://github.com/ICGC-TCGA-PanCancer/CGP-Somatic-Docker/blob/develop/Dockstore.cwl#L10-L14
Encounter warnin…
-
Hi,
Not an issue, but a question regarding TCGA batch-corrected expression data. Where i can download the most recent batch corrected pancancer TCGA RNA-seq expression data? Not individual cancers,…
-
Hi, I get an error as follow:
1,
my command: ~/miniconda3/envs/OSCC/bin/methplotlib -m /NAS/wg_xialin/pancancer/raw_data/oral/fast5/yyl.T/yyl.T_methy.tsv /NAS/wg_hl/pancancer/OSCC/Methylation/f5c…
-
I'm in an interactive session on a linux cluster.
$use Java-11
$use R-4.1
$R
> d library(Seurat)
> library(Matrix)
> d # Extract expression matrix and gene metadata
> expression_matrix gen…
-
We have a gene set derived from the [Nanostring nCounter PanCancer IO 360™ Panel](https://nanostring.com/products/ncounter-assays-panels/oncology/pancancer-io-360/). It's possible to download the gene…
-
I'm exploring the TCGA Pan-Cancer dataset which includes 32 studies. What samples are used as background when I select expression with normalization to normal samples?
Are there adjacent normal sa…
-
I'm trying to follow your walk through with the TCGA PanCancer Head and Neck cancer example but when I try to import data from cBioPortal I get the following error:
I am on a macOS Catalina v10…
-
Hi,
I am trying to run dkfz workflow, it has been running for a few hours but the resource usage was quite low.
some investigations pointed out that SGE is not working
```
roddy@master:/var/spool/…
-
`reports status` and `reports provisioned` seem to rely on AWS libraries, they don't work in azure:
```
$ java -cp reporting.jar info.pancancer.arch3.reportcli.ReportCLI --config config/masterConfig…