Bioconductor Genomicdatacommons

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manifest GDCdownload GenomicDataCommons

16 months ago xiaofeiwang198266 • 0

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TCGA GenomicDataCommons GDC

written 18 months ago by António Miguel de Jesus Domingues ▴ 510

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TCGA GenomicDataCommons

updated 3.1 years ago by Robert Castelo ★ 3.4k • written 3.1 years ago by Hashirama ▴ 10

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GenomicDataCommons

3.4 years ago • updated 3.3 years ago xiaofeiwang18266 ▴ 50

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TCGA GenomicDataCommons

3.8 years ago Ezgi ▴ 60

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GenomicDataCommons R

updated 3.3 years ago by xiaofeiwang18266 ▴ 50 • written 4.9 years ago by gv ▴ 40

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TCGAutils TCGAbiolinks GenomicDataCommons

updated 5.4 years ago by Marcel Ramos 700 • written 5.4 years ago by Dario Strbenac ★ 1.5k

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genomicdatacommons tcga gdc rest http

updated 5.9 years ago by Sean Davis 21k • written 5.9 years ago by mk ▴ 20

8 results • Page 1 of 1

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Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k

For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…

Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0

Thanks for your reply!

Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Hervé Pagès 16k

> I have requested gDNAx developers for a feature request to turn off seqlevelsStyle(txdb) Yes, that's the right course of action. `seqlev…

Comment: ISO a solution to rank-order introns by transcript by mat149 ▴ 80

Hey, In revisiting this question, the following code works for the '+' strand. I am having issues with demarcating intron rank by transcri…

Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by Gordon Smyth 52k

Since the intra-block correlation is negative, it would be best to remove `block` from the model. My experience with genetically identical…

Votes

C: edgeR and lack of counts ID on CPM matrix

A: DESeq2 Following RSEM

A: importing RSEM data into DESeq2

A: Expected counts from RSEM in DESeq2

A: Using RSEM reads for DESeq2

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