Bioconductor Maketxdbfromucsc

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genomicfeatures makeTxDbFromUCSC

updated 7.9 years ago by Michael Lawrence 11k • written 8.4 years ago by federico.comoglio ▴ 100

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genomicfeatures maketxdbfromucsc refseq

updated 7.2 years ago by Hervé Pagès 16k • written 7.2 years ago by Sebastien Vigneau ▴ 10

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genomicfeatures txdb maketxdbfromucsc maketxdbfrombiomart rtracklayer

updated 5.8 years ago by Michael Lawrence 11k • written 5.8 years ago by james.dalgleish ▴ 30

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genomicfeatures R bioconductor maketxdbfromucsc

updated 4.7 years ago by Hervé Pagès 16k • written 4.7 years ago by alanchenslm • 0

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GenomicFeatures makeTxDbFromUCSC

updated 5.2 years ago by shepherl 3.5k • written 5.2 years ago by warrena • 0

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GenomicFeatures makeTxDbFromUCSC R

4.9 years ago DMA1 ▴ 10

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genomicfeatures maketxdbfromucsc

5.8 years ago rbacher ▴ 20

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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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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)

Normalisation of data using DESeq2 with multi-groups

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