Bioconductor Sam

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420

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microarray SAM

updated 4.3 years ago by James W. MacDonald 63k • written 4.3 years ago by xgt1986627 ▴ 10

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845

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SAM samtools pairwisealignment alignment blastn

5.1 years ago ktehmsen • 0

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2.0k

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featurecounts SAM htseqcounts

updated 12 weeks ago by Yang Liao ▴ 380 • written 6.4 years ago by courtney.stairs • 0

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1.2k

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SAM siggenes microarray gene expression sam

6.7 years ago Brian Smith ▴ 120

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1.1k

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differential gene expression sam

updated 7.4 years ago by Aaron Lun ★ 28k • written 7.4 years ago by cirisarri95 • 0

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1.3k

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DEXSeq splicing python SAM

8.0 years ago Fiona ▴ 70

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5.6k

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bam sam alignment biostrings

8.6 years ago ben.ward ▴ 30

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1.1k

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samr SAM siggenes bioconductor differential gene expression

8.7 years ago svlachavas ▴ 810

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1.3k

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r SAM bioconductor

updated 8.7 years ago by Simon Anders ★ 3.7k • written 8.7 years ago by svlachavas ▴ 810

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2.2k

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Limma SAM differential expression

updated 8.9 years ago by James W. MacDonald 63k • written 8.9 years ago by Bade ▴ 310

10 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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