Showing : GDC • reset
0
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11
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2.2k
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TCGAbiolinks GDCquery downloads a file that reads "message": "internal server error"
tcgabiolinks gdc
5.5 years ago jshelton • 0
3
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2
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936
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Difference in TCGA RNAseq expression values between GDC harmonized and legacy data
GDC TCGA tcgabiolinks
updated 5 weeks ago by • 0 • written 3.5 years ago by ▴ 10
0
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2
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2.7k
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Extract gene expression values from GDCprepare object
tcgabiolinks tcga tcgadownload gdcprepare gdc
updated 5.2 years ago by ▴ 260 • written 5.3 years ago by • 0
17
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8
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1.8k
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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
7
votes
7
replies
858
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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 3.6 years ago by 21k • written 3.6 years ago by ▴ 40
4
votes
2
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537
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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
1
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2
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586
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TCGA MAF (Mutations) data
TCGA MAF GDC snp mutations
updated 3.0 years ago by 21k • written 3.0 years ago by ▴ 160
0
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1
reply
2.0k
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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
4.1 years ago pfrancislyon • 0
0
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4
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460
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problem for downloading TCGA data by TCGAbiolikns package
TCGAbiolinks TCGA GDC
2.5 years ago modarzi ▴ 10
0
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0
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286
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Filter TCGAbiolinks by Gene in Query
tcgabiolinks filtering gdc TCGABiolinks rnaseq
2.3 years ago jam526 • 0
0
votes
0
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306
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Problem for downloading TCGA cancer data by TCGAbiolinks
TCGAbiolinks GDC TCGA
2.4 years ago modarzi ▴ 10
11 results • Page 1 of 1
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Comment: Warnings when using "ashr" in lfcshrinkage for DESeq2 by andrebolerbarros ▴ 10
Hi Michael, I'm using the "contrast" parameter, so I cannot use apeglm with that, as far as I know. The "coef" will not allow me to do eve…
Comment: Transcript-level differential expression using DESeq2 by Michael Love 36k
So the way the p-values are generated (non-parametric) you won't get a ranking among these that are highly significant. You can use logFC. …
Answer: Warnings when using "ashr" in lfcshrinkage for DESeq2 by Michael Love 36k
Note sure why it's having difficulty converging. You could use apeglm?
Comment: performing the differential binding in ChIP-seq by ATpoint ★ 1.2k
Cross-posted https://www.biostars.org/p/9524012/#9524012
Comment: Transcript-level differential expression using DESeq2 by Ekta • 0
Yes, i tried that. I used salmon bootstraps also for the same RNAseq data to run Swish and performed the Differential transcript expressio…
Votes
Answer: how to make a group to apply the data to CAMERA
Answer: how to make a group to apply the data to CAMERA
Comment: Using vegan::betadisper for determing if I subset my design for DESeq2
Answer: How to best visualize multi-level transcriptomics experiment data?
A: Interpreting results of sample-to-sample PCA/clustering and changing assignment
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