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DESeq2 Transcriptomics tximport deseq txi

updated 8 months ago by Dario Strbenac ★ 1.5k • written 8 months ago by Hicham ▴ 10

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TxDb.Sscrofa.UCSC.susScr11.refGene TxDb txi

updated 10 months ago by James W. MacDonald 63k • written 10 months ago by Luke • 0

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tx2gene txi error

updated 4.4 years ago by James W. MacDonald 63k • written 4.4 years ago by eliztran • 0

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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 > …

Comment: Suggested package missing from Development version of Bioconductor by shepherl 3.5k

Is your package in review or already in Bioconductor? Its harder if it is in review because we can't tell that the package has or can build…

Comment: biomaRt code/getBM function no longer importing 'coding' sequence via seqType ar by andrew.b.kleist • 0

This worked perfectly! I was able to retrieve the sequences of interest using ```host="https://grch37.ensembl.org"``` within the useEnsembl…

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Comment: DiffBind: dba.plotProfile(profiles)

Normalisation of data using DESeq2 with multi-groups

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