Showing : genomicdatacommons • reset
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How to obtain clinical data from TCGA via Bioconductor GenomicDataCommons
TCGA GenomicDataCommons
updated 8 weeks ago by ★ 2.8k • written 8 weeks ago by ▴ 10
4
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4
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2 questions: why there is nothing for file_ids? How could I generate a manifest file with filtering of Race and Ethnicity?
GenomicDataCommons
5 months ago xiaofeiwang18266 ▴ 40
0
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Getting number of cases added by date to TCGA project with `GenomicDataCommons`
TCGA GenomicDataCommons
10 months ago Ezgi ▴ 30
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4
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extract TCGA barcodes and sample_type information from uuids
GenomicDataCommons R
updated 5 months ago by ▴ 40 • written 23 months ago by ▴ 40
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1.6k
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Matching TCGA Aliquot ID to UUID or Barcode
TCGAutils TCGAbiolinks GenomicDataCommons
updated 2.5 years ago by 550 • written 2.5 years ago by ★ 1.5k
4
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GenomicDataCommons request timeouts when cases() %>% ... %>% results_all()
genomicdatacommons tcga gdc rest http
updated 3.0 years ago by 21k • written 3.0 years ago by ▴ 20
6 results • Page 1 of 1
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Comment: Multi-factor paired RNAseq differential analysis with DEseq2 by swbarnes2 ▴ 970
You can have as many columns as you like in coldata, only those specified in the design will be used when you do the DESeq command So sur…
Comment: Multi-factor paired RNAseq differential analysis with DEseq2 by Matthew • 0
Thanks for the suggestion, I'll give that a try! Based on the PCA, all three factors do tend to influence the results, so I'll try the colu…
Comment: fgsea not downloading due to new r version. Is there a way around this? by amir.khan • 0
Seems to have done the trick and worked. thanks!
Comment: Multi-factor paired RNAseq differential analysis with DEseq2 by Michael Love 35k
Just to underscore swbarnes2 advice above, I'd also recommend discussing statistical design with a local statistician or someone familiar w…
Answer: Multi-factor paired RNAseq differential analysis with DEseq2 by swbarnes2 ▴ 970
First, I'd start by looking at all your samples in PCA. Does sex have a strong effect? Does it make sense to compare one tissue with anot…
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Answer: fgsea not downloading due to new r version. Is there a way around this?
Comment: Unable to install Rhtslib in R-4.1.1
Answer: fgsea not downloading due to new r version. Is there a way around this?
Answer: Swish with more than two conditions. Add support for contrasts?
Answer: ERROR: unable to find an inherited method for function ‘dispersions<-’ for signa
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