Bioconductor Peaks

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ATACSeq peaks ATAC ChIPpeakAnno

11 months ago Raghad • 0

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Peaks MAC2 DiffBind

3.8 years ago Yuan Tian ▴ 290

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nucleosome peaks error Job

updated 5.4 years ago by James W. MacDonald 68k • written 5.4 years ago by anne.kannengiesser • 0

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diffbind chipseq counts peaks bedtools

updated 4.0 years ago by Rory Stark ★ 5.2k • written 7.0 years ago by Ni-Ar ▴ 10

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diffbind chipseq peaks dba is.na

7.0 years ago maria.kondili ▴ 10

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bioconductor annotation peaks

updated 7.4 years ago by Sean Davis 21k • written 7.4 years ago by schaud24 ▴ 10

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Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis by donnycrimson • 0

One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…

Comment: DESeq2 Design controlling for gender by donnycrimson • 0

On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…

Comment: MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list' by donnycrimson • 0

Have you considered streamlining how you handle data input to mitigate these issues. It might help to define the parameters more strictly …

Comment: CluserProfiler message "No gene can be mapped" by Carolina • 0

There is, the overlap that reads out is ( Genes in common: 368 of 368 ). Here is the link for [background genes][1], [term2gene][2], [term2…

Comment: Differing results with DESeq2 by JKim • 0

My two cents. I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for …

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remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline

How to remove X & Y chromosome genes from RNAseq data

Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?

A: Unbalanced experiment with multiple samples from each patient.

A: Understanding contrasts limma

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