Showing : gdc • reset
0
votes
2
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4.7k
views
Extract gene expression values from GDCprepare object
tcgabiolinks tcga tcgadownload gdcprepare gdc
updated 8.8 years ago by ▴ 260 • written 9.0 years ago by • 0
19
votes
8
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4.7k
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How to check the read length for all the TCGA data samples in GDC?
gdc tcga wes gdc data
updated 7.7 years ago by 21k • written 7.7 years ago by ▴ 120
0
votes
11
replies
4.4k
views
TCGAbiolinks GDCquery downloads a file that reads "message": "internal server error"
tcgabiolinks gdc
9.2 years ago jshelton • 0
0
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1
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4.2k
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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
7.8 years ago pfrancislyon • 0
3
votes
2
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3.5k
views
Difference in TCGA RNAseq expression values between GDC harmonized and legacy data
GDC TCGA tcgabiolinks
updated 3.8 years ago by • 0 • written 7.2 years ago by ▴ 10
7
votes
7
replies
2.3k
views
Using GenomicDataCommons R package to identify cases with both DNA methylation and gene expression data
R gdc rna-seq dna methylation
updated 7.2 years ago by 21k • written 7.2 years ago by ▴ 50
1
vote
2
replies
2.0k
views
TCGA MAF (Mutations) data
TCGA MAF GDC snp mutations
updated 6.7 years ago by 21k • written 6.7 years ago by ▴ 160
0
votes
4
replies
2.0k
views
problem for downloading TCGA data by TCGAbiolikns package
TCGAbiolinks TCGA GDC
6.1 years ago modarzi ▴ 10
4
votes
2
replies
1.7k
views
GenomicDataCommons request timeouts when cases() %>% ... %>% results_all()
genomicdatacommons tcga gdc rest http
updated 7.0 years ago by 21k • written 7.0 years ago by ▴ 20
0
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0
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1.7k
views
Filter TCGAbiolinks by Gene in Query
tcgabiolinks filtering gdc TCGABiolinks rnaseq
6.0 years ago jam526 • 0
0
votes
0
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1.1k
views
Problem for downloading TCGA cancer data by TCGAbiolinks
TCGAbiolinks GDC TCGA
6.1 years ago modarzi ▴ 10
0
votes
1
reply
1.0k
views
GenomicDataCommons: Retrieve patient data for RPPA samples
TCGA GenomicDataCommons GDC
written 2.5 years ago by ▴ 510
12 results • Page 1 of 1
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Comment: Joining different datasets and analyzing using the group-specific condition effe by jason.chai • 0
Thank you very much. I had read that and wondered if I used the recommendation in DESeq vignette, I would lose the pairing between groups? …
Comment: Questions about bacon QC and correction on EWAS results by sup0903 • 0
This is qq plot and histogram generated before bacon correction ![enter image description here][1] ![enter image description here][2] …
Comment: Ensembl site unresponsive via biomaRt by sebastianenewell • 0
> I think this is an unrelated issue. The original post includes the > message Error: 'curl_parse_url' is not an exported object from > 'na…
Comment: Development of MSstat workflow to analyze DIA time series data by Gordon Smyth 53k
Are there any other explanatory factors or covariates in your experiment other than time point? Do you have biological replicates at each t…
Answer: Question about the filterByExpr function inputs in edgeR by Gordon Smyth 53k
Either of these choices is perfectly acceptable from an edgeR analysis point of view, it is more to do with which is more relevant for your…
Votes
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
Answer: Clarification on counting in Rsubread (featureCounts)
Comment: Clarification on counting in Rsubread (featureCounts)
C: ControlGenes/ housekeeping genes Deseq2
Answer: Clarification on counting in Rsubread (featureCounts)
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