Bioconductor Samr

Showing : samr • reset

votes

2.9k

views

samr

updated 8.5 years ago by daniel.vantwisk ▴ 50 • written 8.5 years ago by tommykeves • 0

votes

replies

2.1k

views

samr

updated 9.8 years ago by Valerie Obenchain ★ 6.8k • written 9.8 years ago by Linda Chaba ▴ 10

vote

1.5k

views

samr

10.2 years ago SamGG ▴ 360

votes

1.1k

views

samr

updated 10.4 years ago by James W. MacDonald 68k • written 10.4 years ago by yuan.qing ▴ 10

votes

replies

1.7k

views

samr SAM siggenes bioconductor differential gene expression

10.8 years ago svlachavas ▴ 840

vote

3.4k

views

samr rnaseq CRAN

updated 11.1 years ago by Martin Morgan 25k • written 11.1 years ago by aristotele_m ▴ 40

6 results • Page 1 of 1

Recent ...

Replies

Comment: Getting a large intercept with DESeq2 by Michael Love 43k

Thanks James -- Denise you can check the "note on factor levels" in the vignette. And I'd recommend `plotCounts()` for looking at individu…

Comment: Getting a large intercept with DESeq2 by James W. MacDonald 68k

As a trivial example, consider this: ``` > model.matrix(~Treatment, data.frame(Treatment = factor(rep(1:3, each = 4)))) (Intercept) Tre…

Answer: Getting a large intercept with DESeq2 by James W. MacDonald 68k

The default parameterization in R is a treatment-contrasts parameterization that sets one of your groups as the baseline. So the intercept …

Answer: Must I do pseudobulk analysis on Cell Surface Protein Labeling data of Single C by ATpoint ★ 5.0k

There is no "MUST", but pseudobulk aggregation is beneficial to a) enable use of tested and robust methods such as limma (though it could u…

Answer: Post translational modifications and phosphoproteomics in limpa? by Gordon Smyth 53k

Yes, we use limpa for PTMs ourselves. I assume your data is preprocessed so that each row corresponds to a PTM. You replace dpcQuant() with…

Votes

Answer: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif

Using edgeR or DESeq2 to analyze allele-specific expression?

Answer: DESeq2 design for haplotype MPRA

Answer: Failure to download resources (MeSHDb) from AnnotationHub

Awards • All

Popular Question to Stephen Piccolo ▴ 600