Bioconductor Gdc

Showing : gdc • reset

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gdc tcga wes gdc data

updated 7.8 years ago by Sean Davis 21k • written 7.8 years ago by Biologist ▴ 120

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2.4k

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R gdc rna-seq dna methylation

updated 7.3 years ago by Sean Davis 21k • written 7.3 years ago by RichardJActon ▴ 50

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genomicdatacommons tcga gdc rest http

updated 7.0 years ago by Sean Davis 21k • written 7.0 years ago by mk ▴ 20

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GDC TCGA tcgabiolinks

updated 3.8 years ago by cute scientist • 0 • written 7.2 years ago by Antonio Ahn ▴ 10

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TCGA MAF GDC snp mutations

updated 6.7 years ago by Sean Davis 21k • written 6.7 years ago by mario.zanfardino ▴ 160

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tcgabiolinks filtering gdc TCGABiolinks rnaseq

6.0 years ago jam526 • 0

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tcgabiolinks gdc

9.2 years ago jshelton • 0

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1.0k

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TCGA GenomicDataCommons GDC

written 2.6 years ago by António Miguel de Jesus Domingues ▴ 510

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4.8k

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tcgabiolinks tcga tcgadownload gdcprepare gdc

updated 8.8 years ago by Tiago Chedraoui Silva ▴ 260 • written 9.0 years ago by enigmargs • 0

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tcgabiolinks tcga-brca gdc pam50 rna-seq

7.8 years ago pfrancislyon • 0

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TCGAbiolinks TCGA GDC

6.1 years ago modarzi ▴ 10

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TCGAbiolinks GDC TCGA

6.1 years ago modarzi ▴ 10

12 results • Page 1 of 1

Recent ...

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Comment: Combining two proteomics datasets with limpa by Andrew Pattison • 0

Thanks heaps Gordon. I went with option 1 and no normalisation and all seems to have worked well. Cheers, Andrew

Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k

Flagging protein groups as likely contaminants in this way will be fine for a limpa analysis. The `Cont_` proteins can optionally stay in f…

Answer: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Gordon Smyth 53k

Aaron Lun was a PhD student in my Lab back in 2015, when he posted the answers about allele-specific expression that you and Mike Love have…

Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Michael Love 43k

You just need the mouse identifier (controls baseline) and the group specific allelic effect.

Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Julia Broadbent • 0

Hi Emily, Just sharing a resource for handling contaminants - we use the methods described in [Frankenfield et al. (2022)](https://pubs.acs…

Votes

A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen

Comment: limpa analysis advice

Answer: When to use edgeR or limma

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