User: DBScan

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DBScan20
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b****************@gmx.net

Posts by DBScan

<prev • 11 results • page 1 of 2 • next >
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Comment: C: ChIPQC error when running example from documentation
... I'm an idiot, should have read the tutorial more carefully. The hypo however is also included in the tutorial. ...
written 4 weeks ago by DBScan20
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ChIPQC error when running example from documentation
... I want to use ChIPQC for my own ChIP-Seq samples. I followed to code from the here (example 1, page 3&4): https://bioconductor.org/packages/release/bioc/vignettes/ChIPQC/inst/doc/ChIPQC.pdf ``` library(ChIPQC) samples = read.csv(file.path(system.file("extdata", package="ChIPQC"), "example_QCexp ...
R chip-seq chipqc written 4 weeks ago by DBScan20 • updated 4 weeks ago by jared.andrews077.6k
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Answer: A: Deeptools installation fails (Could not find a version that satisfies the requir
... So I fixed it by installing conda. However I couldn't install deeptols in the base environment and therefore had to create a new one. But now R always uses the base environment and therefore can't find deeptools. How can I solve this problem? Running the R-script directly in the terminal with Rscrip ...
written 5 weeks ago by DBScan20
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Deeptools installation fails (Could not find a version that satisfies the requirement matplotlib>=3.1.0)
... I am trying to install deeptools, but I always get the following error: Collecting deeptools Using cached https://files.pythonhosted.org/packages/f6/f3/789edda975fcca4736fab2007d82cab2e86739901c88bb0528db5c338d1f/deepTools-3.5.0.tar.gz Collecting numpy>=1.9.0 (from deeptools) ...
deeptools python3 ubuntu written 6 weeks ago by DBScan20
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Answer: A: GSVA on enrichment scores about R project
... The first error is because "gene" is a data.frame instead of a matrix (I had the same error same days ago too). The second error is because the GMT file has a wrong format I think. You can check the GMT format here: http://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats ...
written 11 weeks ago by DBScan20
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Comment: C: Calculating pathway activity from TCGA RPPA data
... Thanks, I also thought about this procedure. What could be a way to make use of measurements where they measured both (non)-phosphorylated proteins? Manually checking databases like KEGG to see what influence the phosphorylated protein has? ...
written 11 weeks ago by DBScan20
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Calculating pathway activity from TCGA RPPA data
... Is it possible to infer pathway activity from RPPA (reverse-phase protein array) data from for instance TCGA? I've read some papers where they say it is possible, but unfortunately they don't explain how. ...
pathway R tcga rppa written 11 weeks ago by DBScan20 • updated 11 weeks ago by Kevin Blighe66k
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Answer: A: Getting error while installing other packages in R after installing Rtools40 pac
... Isn't Rtools 40 only for R version 4? Maybe you have to upgrade R first to 4, and then install Rtools40. ...
written 3 months ago by DBScan20
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Comment: C: awk column number is a variable
... The output of echo "($colnr)" is ( 281) Why is it that way? ...
written 3 months ago by DBScan20 • updated 3 months ago by Pierre Lindenbaum131k
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awk column number is a variable
... I am trying to filter GTEx for liver tissue. I was able to extract the sample names from the "SamplesAtrributesDS.txt" file and find the corresponding column number in the "transcript_expected_count.gct" file for each sample. I then want to use awk to extract the counts from the column number, but I ...
awk rna-seq bash written 3 months ago by DBScan20 • updated 3 months ago by user_without_id150

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