Bioconductor Gdc

Showing : gdc • reset

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3.9k

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gdc tcga wes gdc data

updated 6.9 years ago by Sean Davis 21k • written 6.9 years ago by Biologist ▴ 120

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1.9k

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R gdc rna-seq dna methylation

updated 6.4 years ago by Sean Davis 21k • written 6.4 years ago by RichardJActon ▴ 50

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1.4k

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genomicdatacommons tcga gdc rest http

updated 6.2 years ago by Sean Davis 21k • written 6.2 years ago by mk ▴ 20

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2.7k

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GDC TCGA tcgabiolinks

updated 2.9 years ago by cute scientist • 0 • written 6.3 years ago by Antonio Ahn ▴ 10

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1.7k

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TCGA MAF GDC snp mutations

updated 5.9 years ago by Sean Davis 21k • written 5.9 years ago by mario.zanfardino ▴ 160

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1.3k

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tcgabiolinks filtering gdc TCGABiolinks rnaseq

5.2 years ago jam526 • 0

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3.8k

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tcgabiolinks gdc

8.4 years ago • updated 8.3 years ago jshelton • 0

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824

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TCGA GenomicDataCommons GDC

written 21 months ago by António Miguel de Jesus Domingues ▴ 510

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4.2k

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tcgabiolinks tcga tcgadownload gdcprepare gdc

updated 8.0 years ago by Tiago Chedraoui Silva ▴ 260 • written 8.1 years ago by enigmargs • 0

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3.5k

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tcgabiolinks tcga-brca gdc pam50 rna-seq

7.0 years ago pfrancislyon • 0

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1.6k

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TCGAbiolinks TCGA GDC

5.3 years ago modarzi ▴ 10

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934

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TCGAbiolinks GDC TCGA

5.3 years ago modarzi ▴ 10

12 results • Page 1 of 1

Recent ...

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Comment: DiffBind custom normalization factor by Abbie • 0

Hello! Thanks so much for adding dba.normalize and all the documentation in the manual! I'm hoping I can ask a follow-up question here. I…

Answer: CpGs with genomic positions greater than the chromosome size in EPICv2? by James W. MacDonald 68k

All of the annotation packages provided by Bioconductor are simply repackaging of existing data from one or more sources. In this case, the…

Comment: Using TPM from tximport of Salmon output for singscore by Kent • 0

Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…

Comment: Using TPM from tximport of Salmon output for singscore by Michael Love 43k

For clustering generally we recommend `vst()` see the workflow for example. For working with individual samples, I can see how a scaling/t…

Comment: DESeq2 model - How to test case/control time course model when taking account wi by Michael Love 43k

I'd recommend working with a local statistician or someone familiar with linear models in R. I have to reserve my time on the support site …

Votes

A: Machine learning in R book

Data preparation and Machine learning on time course RNAseq data

Answer: Use of org.Rn.eg.db with GRCr8 reference genome

A: use tximport's countsFromAbundance when using DESeq2

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