Showing : GDC • reset
0
votes
11
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3.2k
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TCGAbiolinks GDCquery downloads a file that reads "message": "internal server error"
tcgabiolinks gdc
7.4 years ago jshelton • 0
3
votes
2
replies
2.1k
views
Difference in TCGA RNAseq expression values between GDC harmonized and legacy data
GDC TCGA tcgabiolinks
updated 2.0 years ago by • 0 • written 5.4 years ago by ▴ 10
17
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8
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3.1k
views
How to check the read length for all the TCGA data samples in GDC?
gdc tcga wes gdc data
updated 6.0 years ago by 21k • written 6.0 years ago by ▴ 110
7
votes
7
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1.5k
views
Using GenomicDataCommons R package to identify cases with both DNA methylation and gene expression data
R gdc rna-seq dna methylation
updated 5.5 years ago by 21k • written 5.5 years ago by ▴ 50
4
votes
2
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1.1k
views
GenomicDataCommons request timeouts when cases() %>% ... %>% results_all()
genomicdatacommons tcga gdc rest http
updated 5.2 years ago by 21k • written 5.2 years ago by ▴ 20
0
votes
2
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3.7k
views
Extract gene expression values from GDCprepare object
tcgabiolinks tcga tcgadownload gdcprepare gdc
updated 7.1 years ago by ▴ 260 • written 7.2 years ago by • 0
1
vote
2
replies
1.3k
views
TCGA MAF (Mutations) data
TCGA MAF GDC snp mutations
updated 4.9 years ago by 21k • written 4.9 years ago by ▴ 160
0
votes
1
reply
491
views
GenomicDataCommons: Retrieve patient data for RPPA samples
TCGA GenomicDataCommons GDC
written 9 months ago by ▴ 490
0
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4
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1.2k
views
problem for downloading TCGA data by TCGAbiolikns package
TCGAbiolinks TCGA GDC
4.4 years ago modarzi ▴ 10
0
votes
0
replies
702
views
Problem for downloading TCGA cancer data by TCGAbiolinks
TCGAbiolinks GDC TCGA
4.3 years ago modarzi ▴ 10
0
votes
0
replies
968
views
Filter TCGAbiolinks by Gene in Query
tcgabiolinks filtering gdc TCGABiolinks rnaseq
4.2 years ago jam526 • 0
0
votes
1
reply
3.0k
views
how to infer missing PAM50 molecular subtypes in TCGA-BRCA dataset downloaded with TCGABiolinks?
tcgabiolinks tcga-brca gdc pam50 rna-seq
6.0 years ago pfrancislyon • 0
12 results • Page 1 of 1
Recent ...
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Comment: Interaction Terms in DESeq2 - Shrinkage by Michael Love 41k
Yes, apeglm requires relevel and nbinomWaldTest to generate the coefficient estimate and its SE. Alternatively you can use ashr with a con…
Comment: A ComBat-seq issue: the covariates are confounded by schlumbohm • 0
Dear ATpoint, thank you for the comment. I did correct the question. For the group, I did accidentally share the input for all three batch…
Comment: Memory errors using read.bismark? by Peter Hickey ▴ 690
If you process serially (i.e. with `BPPARAM = SerialParam()`) then you might be okay. The final object will be on the order of 250 GB in-me…
Answer: blockwiseModule crashes in the end and doesn't generate modules by xaweh28128 • 0
Test your word skills and see if you can crack the code in today's Wordle puzzle. [Nytimes wordle](https://wordlenytimes.net/quordle-game/)…
Comment: Memory errors using read.bismark? by Juan Higareda • 0
Thanks for the answer. Actually, processing one file and keeping it in memory wasn't the problem, is more processing all the 15 files to bu…
Votes
Comment: Not fully paired differential gene expression analysis
Comment: [DiffBind] Obtaining normalization factors
Answer: ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with var
Comment: Not fully paired differential gene expression analysis
Answer: GSVA error
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