Bioconductor Vignette

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SummarizedExperiment vignette

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biomaRt vignette

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software error cellmix vignette expressionset

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github vignette test developers

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vignette

updated 8.2 years ago by Dan Tenenbaum ★ 8.2k • written 8.2 years ago by KB ▴ 50

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

Comment: DiffBind: dba.plotProfile(profiles)

Normalisation of data using DESeq2 with multi-groups

Answer: Normalisation of data using DESeq2 with multi-groups

Answer: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq

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