Bioconductor CIGAR

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2.1k

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GenomicAlignments BAM CIGAR

updated 5.1 years ago by Janet Young ▴ 740 • written 5.1 years ago by Shian Su ▴ 40

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1.5k

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cigar not-implemented-yet

updated 5.2 years ago by Hervé Pagès 16k • written 5.2 years ago by stephen.rudd • 0

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1.1k

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Rsubread cigar

updated 5.2 years ago by Gordon Smyth 52k • written 5.2 years ago by lauren.fitch • 0

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2.6k

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rsamtools alignment cigar

7.5 years ago Frocha ▴ 20

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2.4k

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bsgenome cigar alignment

updated 10.0 years ago by Hervé Pagès 16k • written 10.0 years ago by Stefanie Tauber ▴ 40

5 results • Page 1 of 1

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Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0

Hi Tim, Thanks for your reply! Yes, my data is 450K, and it is TCGA methylation data downloaded by TCGAbiolinks. The problem is that I can …

Answer: Error in get_anno_data(ontology) : ontology not supported yet... by Guido Hooiveld ★ 4.1k

Did you check the help page for the function `enrichDO`? Type `?enrichDO`. I am asking, because there it is stated that the argument `ont`…

Comment: Build error on kunpeng2 Linux aarch64 by martin.grigorov ▴ 10

Hi, There was a problem with `icu` and because of that the (r)curl library was not installed. The system/OS curl library is one version ol…

Answer: Standardization of rlog transformed counts before PCA by ATpoint ★ 4.6k

I guess you mean scaling in terms of Z-scoring? There are plenty of posts towards scaling in PCA both here on Bioconductor and in other com…

Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Tim Peters ▴ 200

Also, re DMR.plot(), yes the understanding is that all DMRs from EPICv2 should be plotted in hg38. I've left that implied for the user sinc…

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Comment: Feature Counts - potential bug with outfile.jcounts

Answer: Feature Counts - potential bug with outfile.jcounts

Comment: Can we get beta values with DMRcate package

Answer: Can we get beta values with DMRcate package

DiffBind giving different results from dba.report() and dba.analyze(..., bRetrieveAnalysis=TRUE)

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Popular Question to martin.grigorov ▴ 10

Scholar to James W. MacDonald 67k