User: nashtf

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nashtf10
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10
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New User
Location:
United States
Last seen:
3 years, 3 months ago
Joined:
4 years ago
Email:
n*****@g.cofc.edu

Posts by nashtf

<prev • 4 results • page 1 of 1 • next >
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Comment: C: I would like to add gene names to a volcano plot obtained from DEseq2
... Can you append the output of `dput(res)` so we can easily recreate the matrix? ...
written 3.3 years ago by nashtf10
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How to receive gene ontology p-value and number of genes from input in biomaRt
... I've been using ToppFunn for gene ontologies and it worked great and fast, but it's a blackbox as to how it gets its results. I'm looking for an open-source, R solution and found biomaRt. I have a few qualms with it, largely it doesn't seem very intuitive as to how one finds the information they nee ...
R biomart written 3.3 years ago by nashtf10
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Is the PAM50 subtype available for TCGA BRCA data?
... I have some UNC Illumina RNAseqV2 data with about 100 genes, 800 patients with UNC ID. I'd like to find the subtype of each tumor (normal, luminal A, luminal B, basal, HER2) for a classifier. Preferably with the UNC ID but if TCGA barcode is provided I believe it's possible to match them up. I can't ...
tcga breast cancer rna-seq written 4.0 years ago by nashtf10 • updated 3.5 years ago by hAjmal30
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Comment: A: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... I tried running this with the BRCA data and get the following error on reading in the merged clinical data: clinical <- t(read.table('Clinical/BRCA.merged_only_clinical_clin_format.txt',header=T,row.names=1,sep='\t')) Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.stri ...
written 4.1 years ago by nashtf10 • updated 2.6 years ago by RamRS24k

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