Showing : GDC • reset
3
votes
2
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923
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Difference in TCGA RNAseq expression values between GDC harmonized and legacy data
GDC TCGA tcgabiolinks
updated 4 weeks ago by • 0 • written 3.5 years ago by ▴ 10
0
votes
0
replies
281
views
Filter TCGAbiolinks by Gene in Query
tcgabiolinks filtering gdc TCGABiolinks rnaseq
2.3 years ago jam526 • 0
0
votes
0
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302
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Problem for downloading TCGA cancer data by TCGAbiolinks
TCGAbiolinks GDC TCGA
2.4 years ago modarzi ▴ 10
0
votes
4
replies
454
views
problem for downloading TCGA data by TCGAbiolikns package
TCGAbiolinks TCGA GDC
2.5 years ago modarzi ▴ 10
1
vote
2
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584
views
TCGA MAF (Mutations) data
TCGA MAF GDC snp mutations
updated 3.0 years ago by 21k • written 3.0 years ago by ▴ 160
4
votes
2
replies
534
views
GenomicDataCommons request timeouts when cases() %>% ... %>% results_all()
genomicdatacommons tcga gdc rest http
updated 3.3 years ago by 21k • written 3.3 years ago by ▴ 20
7
votes
7
replies
854
views
Using GenomicDataCommons R package to identify cases with both DNA methylation and gene expression data
R gdc rna-seq dna methylation
updated 3.6 years ago by 21k • written 3.6 years ago by ▴ 40
17
votes
8
replies
1.8k
views
How to check the read length for all the TCGA data samples in GDC?
gdc tcga wes gdc data
updated 4.1 years ago by 21k • written 4.1 years ago by ▴ 90
0
votes
1
reply
2.0k
views
how to infer missing PAM50 molecular subtypes in TCGA-BRCA dataset downloaded with TCGABiolinks?
tcgabiolinks tcga-brca gdc pam50 rna-seq
4.1 years ago pfrancislyon • 0
0
votes
2
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2.7k
views
Extract gene expression values from GDCprepare object
tcgabiolinks tcga tcgadownload gdcprepare gdc
updated 5.1 years ago by ▴ 260 • written 5.3 years ago by • 0
0
votes
11
replies
2.1k
views
TCGAbiolinks GDCquery downloads a file that reads "message": "internal server error"
tcgabiolinks gdc
5.5 years ago jshelton • 0
11 results • Page 1 of 1
Recent ...
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Answer: Get MANE transcripts from TxDb.Hsapiens.UCSC.hg38.knownGene by James W. MacDonald 59k
There is the ncbiRefSeqSelect table that has the MANE and RefSeq Select transcripts. It's not just the MANE though. ``` > z <- makeTxDb…
Comment: Handling of missing values in limma by AyHi • 0
Thank you, Gordon, for your reply. I used sum(is.na(lmfit)) after lmFit, but somewhat it indicated there was no NA observations even when…
Comment: merging VCF files by lesefo6448 • 0
You can use this VCF Merger Software if you want to Merge VCF files into one file. this Software easily Merge your multiple VCF files with…
Comment: featureCounts: 0% successfully assigned fragments by ATpoint ★ 1.2k
What you have to do is to check whether the chromosome names in the BAM file are part of the GTF. Do it programatically, not by eye. Extrac…
Comment: champ.SVD() error, assumes standard class() function will return single string by Basti ▴ 280
What is class(`yourbeta`) ?
Votes
Answer: Load packages when using BatchtoolsParam
Comment: Load packages when using BatchtoolsParam
Answer: edgeR: the F-statistics changed after removing lowly expressed gene
Answer: edgeR: the F-statistics changed after removing lowly expressed gene
A: DESeq2: thousands of NA for pvalues?
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Scholar to James W. MacDonald 59k
Popular Question to Gyan Prakash Mishra • 0
Scholar to ATpoint ★ 1.2k
Teacher to Gordon Smyth 45k
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