Bioconductor Narrowpeaks

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Rsubread atac-seq narrowpeaks featurecounts

updated 5.9 years ago by Wei Shi ★ 3.5k • written 5.9 years ago by j.bergenstrahle ▴ 80

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Chipseq DNAseq ATAC bayespeak narrowpeaks

updated 8.4 years ago by Gordon Smyth 48k • written 8.4 years ago by samuel collombet ▴ 140

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ChIPSeq chipseq NarrowPeaks ChIPSeq chipseq NarrowPeaks

9.4 years ago Robert Chase ▴ 10

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GO DiffBind NarrowPeaks GO DiffBind NarrowPeaks

9.6 years ago Rory Stark ★ 5.0k

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Answer: Problems with FLOWAI by SHASHI • 0

Additionally, if you're looking to clean FCS data files, you can utilize an R script. I've prepared a comprehensive YouTube tutorial to aid…

Answer: Is SeqSQC compatible with hg38? by James W. MacDonald 63k

I'll answer your question with a question. Is there any reason to believe that things like IBD or PCA or Sex checks would be dependent on t…

Comment: using featureCounts (Subread) to count only spliced reads per gene - behavior of by Gregory • 0

Thanks for the prompt response, Gordon. I'm looking for count at the gene level - the gene id is the meta feature, so one row per gene in …

Comment: DiffBind handling of replicates and consensus by Rory Stark ★ 5.0k

You may want to try different values for the `normalize` parameter: dbObj <- dba.normalize(DBA = dbObj, library = "RiP", normalize=DBA…

Comment: DiffBind: dba.plotProfile(profiles) by Rory Stark ★ 5.0k

Yes, setting `raster_quality` down is a good way to address this issue. I've taken to using `raster_quality=1` in general as I think the pl…

Votes

Answer: How do I merge a list of GRanges?

Comment: biomaRt code/getBM function no longer importing 'coding' sequence via seqType ar

Comment: DiffBind: dba.plotProfile(profiles)

Answer: DiffBind - how to prep the sample matrix when multiple bam files are used by MAC

Comment: DiffBind: dba.plotProfile(profiles)

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