Bioconductor Indel

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votes

replies

991

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PureCN indel somatic germline

updated 6.3 years ago by markus.riester ▴ 130 • written 6.3 years ago by pathkim • 0

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888

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snv granges genomicranges variantannotation indel

updated 7.1 years ago by Michael Lawrence 11k • written 7.1 years ago by addyS • 0

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733

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pairwisealignment indel

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

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1.6k

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indel customprodb fasta variantannotation

updated 8.2 years ago by xiaojing.wang ▴ 50 • written 8.2 years ago by kristenbeck527 • 0

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1.1k

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indel sequencing alignment

8.4 years ago Merienne Nicolas ▴ 120

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1.1k

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rnaseq subjunc indel

updated 8.9 years ago by Wei Shi ★ 3.5k • written 8.9 years ago by daniel.silvestre ▴ 100

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2.5k

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bam indel genomicalignments biostrings

updated 8.9 years ago by Nathaniel Hayden ▴ 180 • written 8.9 years ago by Stefanie Tauber ▴ 40

7 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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