Bioconductor GenomicDataCommons

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manifest GDCdownload GenomicDataCommons

8 months ago xiaofeiwang198266 • 0

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TCGA GenomicDataCommons GDC

written 10 months ago by António Miguel de Jesus Domingues ▴ 490

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TCGA GenomicDataCommons

updated 2.4 years ago by Robert Castelo ★ 3.3k • written 2.4 years ago by Hashirama ▴ 10

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GenomicDataCommons

2.7 years ago xiaofeiwang18266 ▴ 50

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TCGA GenomicDataCommons

3.1 years ago Ezgi ▴ 60

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GenomicDataCommons R

updated 2.7 years ago by xiaofeiwang18266 ▴ 50 • written 4.2 years ago by gv ▴ 40

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TCGAutils TCGAbiolinks GenomicDataCommons

updated 4.8 years ago by Marcel Ramos 690 • written 4.8 years ago by Dario Strbenac ★ 1.5k

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genomicdatacommons tcga gdc rest http

updated 5.3 years ago by Sean Davis 21k • written 5.3 years ago by mk ▴ 20

8 results • Page 1 of 1

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Comment: Deseq2. decontXcounts not integers. Useful alternative? by camp ▴ 10

Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…

Comment: Deseq2. decontXcounts not integers. Useful alternative? by ATpoint ★ 4.0k

I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…

Answer: Improving the design matrices vignette in RNAseq123 by Gordon Smyth 50k

Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…

Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0

Thank you for your comment! I'll review my code from top to bottom.

Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k

So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.

Votes

Comment: Deseq2. decontXcounts not integers. Useful alternative?

Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)

biomaRt error: database disk image is malformed

Comment: biomaRt : No lock file for BiocFileCache

Answer: Cross-species analysis - how to compute the mid parent value?

Awards • All

Scholar to James W. MacDonald 65k

Supporter to JKim • 0