Bioconductor RRBS

Showing : RRBS • reset

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1.7k

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edgeR rrbs

updated 4.7 years ago by Gordon Smyth 48k • written 4.7 years ago by ingerslev • 0

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1.7k

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biseq RRBS SAAP-BS coverage

8.4 years ago maria.maqueda • 0

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835

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edgeR model-selection RRBS mixture-experiment

2.5 years ago ingerslev • 0

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1.6k

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sva RRBS

updated 6.6 years ago by Jeff Leek ▴ 640 • written 6.6 years ago by mrodrigues.fernanda ▴ 10

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1.8k

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methykit rrbs

updated 5.4 years ago by Mike Smith ★ 6.1k • written 5.4 years ago by bekah ▴ 20

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1.6k

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rrbs batch effect methylation sva

updated 7.0 years ago by dashbrook1 • 0 • written 8.2 years ago by GFM ▴ 20

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1.2k

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edgeR methyation RRBS

updated 5.7 years ago by Gordon Smyth 48k • written 5.7 years ago by osa.zuta ▴ 40

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658

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MethylCC RRBS cord blood

3.2 years ago weichen-cls • 0

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1.2k

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limma rrbs bsseq

updated 7.3 years ago by Aaron Lun ★ 28k • written 7.3 years ago by nhejazi • 0

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963

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biseq RRBS betaregression

6.5 years ago l.eijssen • 0

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446

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biseq betaRegression RRBS Methylation

3.5 years ago i.s.castanho • 0

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543

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Biseq Methylation DMP DMR RRBS

3.2 years ago i.s.castanho • 0

12 results • Page 1 of 1

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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…

Comment: DiffBind: dba.plotProfile(profiles) by Dorien ▴ 10

Not really an answer as I don't know really know why , but I also had the same issue and may have found a workaround ! If I set maxSites > …

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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