Showing : gdc • reset
19
votes
8
replies
4.0k
views
How to check the read length for all the TCGA data samples in GDC?
gdc tcga wes gdc data
updated 7.0 years ago by 21k • written 7.0 years ago by ▴ 120
7
votes
7
replies
2.0k
views
Using GenomicDataCommons R package to identify cases with both DNA methylation and gene expression data
R gdc rna-seq dna methylation
updated 6.5 years ago by 21k • written 6.5 years ago by ▴ 50
4
votes
2
replies
1.5k
views
GenomicDataCommons request timeouts when cases() %>% ... %>% results_all()
genomicdatacommons tcga gdc rest http
updated 6.3 years ago by 21k • written 6.3 years ago by ▴ 20
3
votes
2
replies
2.8k
views
Difference in TCGA RNAseq expression values between GDC harmonized and legacy data
GDC TCGA tcgabiolinks
updated 3.0 years ago by • 0 • written 6.4 years ago by ▴ 10
1
vote
2
replies
1.7k
views
TCGA MAF (Mutations) data
TCGA MAF GDC snp mutations
updated 6.0 years ago by 21k • written 6.0 years ago by ▴ 160
0
votes
0
replies
1.4k
views
Filter TCGAbiolinks by Gene in Query
tcgabiolinks filtering gdc TCGABiolinks rnaseq
5.3 years ago jam526 • 0
0
votes
11
replies
3.9k
views
TCGAbiolinks GDCquery downloads a file that reads "message": "internal server error"
tcgabiolinks gdc
8.5 years ago • updated 8.4 years ago jshelton • 0
0
votes
1
reply
840
views
GenomicDataCommons: Retrieve patient data for RPPA samples
TCGA GenomicDataCommons GDC
written 22 months ago by ▴ 510
0
votes
2
replies
4.2k
views
Extract gene expression values from GDCprepare object
tcgabiolinks tcga tcgadownload gdcprepare gdc
updated 8.1 years ago by ▴ 260 • written 8.2 years ago by • 0
0
votes
1
reply
3.6k
views
how to infer missing PAM50 molecular subtypes in TCGA-BRCA dataset downloaded with TCGABiolinks?
tcgabiolinks tcga-brca gdc pam50 rna-seq
7.1 years ago pfrancislyon • 0
0
votes
4
replies
1.6k
views
problem for downloading TCGA data by TCGAbiolikns package
TCGAbiolinks TCGA GDC
5.4 years ago modarzi ▴ 10
0
votes
0
replies
962
views
Problem for downloading TCGA cancer data by TCGAbiolinks
TCGAbiolinks GDC TCGA
5.4 years ago modarzi ▴ 10
12 results • Page 1 of 1
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Comment: Bioconductor 3.20 Release Schedule by randyprice13102000 • 0
This offers much info https://bioconductor.org/checkResults/release/bioc-LATEST/
Comment: Filtering after DESeq by ATpoint ★ 4.8k
The problem is that your prefilter is not group-aware so the behaviour of seeing these sorts of outliers is expected. This is why I always …
Comment: GSEA preranked analysis downstream of DEseq2 by ATpoint ★ 4.8k
All due respect, this is what people do since pvalues exist, so this paper is not a reference, not is this a special score that merits a na…
Comment: Check removeBatchEffect effectiveness by ATpoint ★ 4.8k
> insert size, mean GC, etc... This is not a classical "batch" in the common sense, at least I've never seen this to be corrected for expl…
Answer: Check removeBatchEffect effectiveness by Gordon Smyth 52k
Your call to removeBatchEffect() is not correct because that function does not have an argument called `batch3`, meaning that the batch fac…
Votes
Answer: DiffBind; Error: No sites have activity greater than filter value
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
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