Showing : gdc • reset
0
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2
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3.7k
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Extract gene expression values from GDCprepare object
tcgabiolinks tcga tcgadownload gdcprepare gdc
updated 7.1 years ago by ▴ 260 • written 7.3 years ago by • 0
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11
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3.2k
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TCGAbiolinks GDCquery downloads a file that reads "message": "internal server error"
tcgabiolinks gdc
7.5 years ago jshelton • 0
17
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8
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3.1k
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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
0
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1
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3.0k
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how to infer missing PAM50 molecular subtypes in TCGA-BRCA dataset downloaded with TCGABiolinks?
tcgabiolinks tcga-brca gdc pam50 rna-seq
6.1 years ago pfrancislyon • 0
3
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2
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2.2k
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Difference in TCGA RNAseq expression values between GDC harmonized and legacy data
GDC TCGA tcgabiolinks
updated 2.1 years ago by • 0 • written 5.5 years ago by ▴ 10
7
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7
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1.6k
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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
1
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2
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1.3k
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TCGA MAF (Mutations) data
TCGA MAF GDC snp mutations
updated 5.0 years ago by 21k • written 5.0 years ago by ▴ 160
0
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4
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1.2k
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problem for downloading TCGA data by TCGAbiolikns package
TCGAbiolinks TCGA GDC
4.4 years ago modarzi ▴ 10
4
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2
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1.1k
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GenomicDataCommons request timeouts when cases() %>% ... %>% results_all()
genomicdatacommons tcga gdc rest http
updated 5.3 years ago by 21k • written 5.3 years ago by ▴ 20
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0
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983
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Filter TCGAbiolinks by Gene in Query
tcgabiolinks filtering gdc TCGABiolinks rnaseq
4.3 years ago jam526 • 0
0
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0
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715
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Problem for downloading TCGA cancer data by TCGAbiolinks
TCGAbiolinks GDC TCGA
4.4 years ago modarzi ▴ 10
0
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1
reply
507
views
GenomicDataCommons: Retrieve patient data for RPPA samples
TCGA GenomicDataCommons GDC
written 10 months ago by ▴ 510
12 results • Page 1 of 1
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Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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