Bioconductor DESEQ

Showing : DESEQ • reset

votes

replies

339

views

deseq DESeq2

updated 4 months ago by ATpoint ★ 4.1k • written 4 months ago by Hugo • 0

votes

replies

892

views

DESeq DESeq2

updated 9 months ago by ATpoint ★ 4.1k • written 9 months ago by Abir.khazaal ▴ 10

votes

655

views

Z-score RNASeqData Deseq DESeq2

updated 7 months ago by James W. MacDonald 65k • written 7 months ago by khaserdene99 • 0

votes

replies

523

views

deseq DESeq2

5 months ago georgii.vdovin • 0

vote

replies

318

views

DESeq2 deseq

10 weeks ago Meme • 0

votes

replies

658

views

DESeq2 apeglm DESeq ApeGLM Ashr

updated 9 months ago by Michael Love 41k • written 9 months ago by Ndimensional ▴ 20

votes

replies

26k

views

deseq deseq2

updated 9 months ago by Erika • 0 • written 9.3 years ago by c.lieftink@nki.nl ▴ 40

votes

383

views

Deseq DESeq2

updated 5 months ago by Michael Love 41k • written 6 months ago by georgii.vdovin • 0

8 results • Page 1 of 1

Recent ...

Replies

Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0

Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …

Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k

Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…

Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k

I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …

Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k

It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …

Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k

This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…

Votes

Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-

Answer: limma Intercept vs No-intercept models completely changing DMR results?

Answer: CombineArrays for EPIC and EPIC V2

Answer: Too many significant genes when integrating gtex and tcga

Comment: Too many significant genes when integrating gtex and tcga

Awards • All