Bioconductor Gdc

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3.2k

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tcgabiolinks gdc

7.5 years ago • updated 7.4 years ago jshelton • 0

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3.1k

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gdc tcga wes gdc data

updated 6.0 years ago by Sean Davis 21k • written 6.0 years ago by Biologist ▴ 110

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1.6k

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R gdc rna-seq dna methylation

updated 5.5 years ago by Sean Davis 21k • written 5.5 years ago by RichardJActon ▴ 50

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1.2k

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TCGAbiolinks TCGA GDC

4.4 years ago modarzi ▴ 10

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1.1k

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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

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tcgabiolinks tcga tcgadownload gdcprepare gdc

updated 7.1 years ago by Tiago Chedraoui Silva ▴ 260 • written 7.2 years ago by enigmargs • 0

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2.1k

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GDC TCGA tcgabiolinks

updated 2.0 years ago by cute scientist • 0 • written 5.4 years ago by Antonio Ahn ▴ 10

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1.3k

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TCGA MAF GDC snp mutations

updated 5.0 years ago by Sean Davis 21k • written 5.0 years ago by mario.zanfardino ▴ 160

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3.0k

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tcgabiolinks tcga-brca gdc pam50 rna-seq

6.1 years ago pfrancislyon • 0

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497

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TCGA GenomicDataCommons GDC

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

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709

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TCGAbiolinks GDC TCGA

4.4 years ago modarzi ▴ 10

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974

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tcgabiolinks filtering gdc TCGABiolinks rnaseq

4.3 years ago jam526 • 0

12 results • Page 1 of 1

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Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k

> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …

Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10

With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.

Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k

You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.

Answer: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k

Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…

Comment: get BM error by James W. MacDonald 65k

I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…

Votes

Answer: How to retrieve gene ontology GO class from gene list?

C: when to apply quantile normalization with voom in limma/voom framework with RNA-

A: How to know if I should use voomWithQualityWeights() or not?

A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom

Awards • All

Teacher to Gordon Smyth 50k