Bioconductor Batch Correction

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1.4k

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SC3 Scater Scran scRNA-Seq Batch Correction

updated 4.5 years ago by Vladimir Kiselev ▴ 150 • written 4.5 years ago by hamza_karakurt ▴ 50

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1.0k

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deseq2 differential expression batch correction

updated 4.3 years ago by Michael Love 40k • written 4.3 years ago by wunderl ▴ 40

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710

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Diffbind ATAC batch correction blocking factor

updated 4.1 years ago by Rory Stark ★ 5.0k • written 4.1 years ago by rm1238 • 0

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461

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DESeq2 batch correction

updated 3.9 years ago by James W. MacDonald 63k • written 3.9 years ago by MT ▴ 10

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1.2k

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scrna-seq integration batch correction

updated 3.7 years ago by Aaron Lun ★ 28k • written 3.7 years ago by p.joshi ▴ 40

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820

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deseq2 differential expression batch correction design

updated 4.3 years ago by Michael Love 40k • written 4.3 years ago by wunderl ▴ 40

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708

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methylation ComBat Linear models batch correction AIC

updated 3.8 years ago by Kevin Blighe 3.8k • written 3.8 years ago by lucasmiranda42 • 0

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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 > …

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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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