Bioconductor Timecourse

Showing : timecourse • reset

votes

replies

167

views

DESeq2 timecourse DifferentialExpression

updated 29 days ago by James W. MacDonald 65k • written 29 days ago by joshua.mannheimer • 0

votes

242

views

DESeq2 timecourse time

updated 3 months ago by Michael Love 41k • written 3 months ago by Anastasiia • 0

votes

269

views

RNASeq DESeq2 timecourse

3 months ago WS • 0

vote

replies

2.7k

views

limma edger timecourse without replicate voom

written 7.5 years ago by Camila Orellana ▴ 10

vote

replies

916

views

time-series DESeq2 RNASeq timecoursedata TimeCourse

updated 8 months ago by ATpoint ★ 4.1k • written 8 months ago by Debebe • 0

votes

510

views

timecoursedata RNASeqData TimeCourse DESeq2

updated 9 months ago by Michael Love 41k • written 9 months ago by georgii.vdovin • 0

votes

replies

1.3k

views

Transcriptomics TimeCourse DESeq2

updated 9 months ago by Michael Love 41k • written 10 months ago by smac97 • 0

votes

562

views

timecourse KEGG DESeq2

updated 11 months ago by Michael Love 41k • written 11 months ago by Fred • 0

votes

replies

1.4k

views

deseq2 timecourse design and contrast matrix

updated 8 weeks ago by ta_awwad ▴ 10 • written 8.5 years ago by Assa Yeroslaviz ★ 1.5k

9 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