Showing : gdc • reset
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
7.4 years ago jshelton • 0
3
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2
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2.1k
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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
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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
7
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7
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1.5k
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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
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 5.2 years ago by 21k • written 5.2 years ago by ▴ 20
0
votes
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 7.2 years ago by • 0
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 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
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problem for downloading TCGA data by TCGAbiolikns package
TCGAbiolinks TCGA GDC
4.4 years ago modarzi ▴ 10
0
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0
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703
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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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0
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968
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Filter TCGAbiolinks by Gene in Query
tcgabiolinks filtering gdc TCGABiolinks rnaseq
4.2 years ago jam526 • 0
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
6.0 years ago pfrancislyon • 0
12 results • Page 1 of 1
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Replies
Comment: How to retrieve detailed regression results from deseq2 by Weiqian ▴ 10
Hi Michael, thanks for the answer! I'll have a look : )
Comment: DESeq filtering specific to contrasts by Michael Love 41k
It will likely not filter it out, but really the per-dataset details would affect the results.
Comment: DESeq filtering specific to contrasts by Carlin95 • 0
Thanks for clarifying. Could I ask maybe one more thing for my sanity? Let's say you had a multi-factor experiment with contrasts including…
Comment: FilterByExpr low counts with small sample size by Jonathan ▴ 10
Thank you for your answer; However, I have some follow-up questions. Following up in In your [1-2-3 article][1], you say that > "... the…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Seyram M. • 0
Thank you very much for your reply! I will do so. Kind regards, Seyram
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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