Showing : GDC • reset
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GenomicDataCommons: Retrieve patient data for RPPA samples
TCGA GenomicDataCommons GDC
written 17 months ago by ▴ 510
3
votes
2
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2.4k
views
Difference in TCGA RNAseq expression values between GDC harmonized and legacy data
GDC TCGA tcgabiolinks
updated 2.6 years ago by • 0 • written 6.0 years ago by ▴ 10
0
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0
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1.2k
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Filter TCGAbiolinks by Gene in Query
tcgabiolinks filtering gdc TCGABiolinks rnaseq
4.8 years ago jam526 • 0
0
votes
0
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845
views
Problem for downloading TCGA cancer data by TCGAbiolinks
TCGAbiolinks GDC TCGA
5.0 years ago modarzi ▴ 10
0
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4
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1.4k
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problem for downloading TCGA data by TCGAbiolikns package
TCGAbiolinks TCGA GDC
5.0 years ago modarzi ▴ 10
1
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2
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1.5k
views
TCGA MAF (Mutations) data
TCGA MAF GDC snp mutations
updated 5.5 years ago by 21k • written 5.5 years ago by ▴ 160
4
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2
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1.3k
views
GenomicDataCommons request timeouts when cases() %>% ... %>% results_all()
genomicdatacommons tcga gdc rest http
updated 5.8 years ago by 21k • written 5.8 years ago by ▴ 20
7
votes
7
replies
1.8k
views
Using GenomicDataCommons R package to identify cases with both DNA methylation and gene expression data
R gdc rna-seq dna methylation
updated 6.1 years ago by 21k • written 6.1 years ago by ▴ 50
19
votes
8
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3.7k
views
How to check the read length for all the TCGA data samples in GDC?
gdc tcga wes gdc data
updated 6.6 years ago by 21k • written 6.6 years ago by ▴ 120
0
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1
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3.3k
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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
6.6 years ago pfrancislyon • 0
0
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2
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4.0k
views
Extract gene expression values from GDCprepare object
tcgabiolinks tcga tcgadownload gdcprepare gdc
updated 7.7 years ago by ▴ 260 • written 7.8 years ago by • 0
0
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11
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3.5k
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TCGAbiolinks GDCquery downloads a file that reads "message": "internal server error"
tcgabiolinks gdc
8.0 years ago jshelton • 0
12 results • Page 1 of 1
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Answer: Deseq2 res Function by Michael Love 43k
> Does this mean the young and KO groups were numerators and denominators in the analysis, respectively? Read over the vignette and work…
Answer: ANOVA like approach of edgeR by Gordon Smyth 51k
You need to clarify whether interactions are present for the two factors in your study. In the two factors do not interact, then the code y…
Answer: Create Illmina bead summary data by Gordon Smyth 51k
GenomeStudio produces IDAT files that you can read using the `read.idat` function in limma. That is the recommended way to read GenomeStudi…
Comment: Help with RSEM counts: do I transpose matrix? by NB • 0
OK thank you.
Comment: Help with RSEM counts: do I transpose matrix? by James W. MacDonald 67k
You can ask here, but please read the `DESeq2` vignette first, which should answer most questions.
Votes
Answer: Deseq2 res Function
Answer: BiocNeighbours Utility for k-Nearest Neighbour Classification
Answer: ANOVA like approach of edgeR
Answer: ANOVA like approach of edgeR
Comment: ANOVA like approach of edgeR
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