Bioconductor Annotatepeak

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GRanges ChIPseeker annotatePeak TxDb EnsDb

updated 6.7 years ago by Johannes Rainer ★ 2.1k • written 6.7 years ago by foehn ▴ 100

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chipseeker annotatepeak

updated 8.0 years ago by Guangchuang Yu ★ 1.2k • written 8.0 years ago by Wojeff • 0

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genomicranges granges iranges annotatepeak

updated 9.5 years ago by Michael Lawrence ★ 11k • written 9.5 years ago by Dimitris Polychronopoulos ▴ 80

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annotatePeak chipseeker chipseq org.Mm.eg.db TxDb.Mmusculus.UCSC.mm9.knownGene

updated 10.1 years ago by Martin Morgan 25k • written 10.3 years ago by Elsa • 0

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Comment: copy number/LOH for Affy 100K by igkryycpinmshzugby • 0

Hi John For copy number and LOH analysis from Affymetrix 100K SNP arrays you can use aroma.affymetrix or CRLMM packages in Bioconductor. …

Comment: Integration: Paired-end vs healthy single-end from a different source by igkryycpinmshzugby • 0

Yes, Option 1 (technical homogenization) reprocessing paired-end samples as single-end using only R1 is the most defensible approach when l…

Answer: Integration: Paired-end vs healthy single-end from a different source by James W. MacDonald 68k

If by reprocess you mean generate libraries and re-sequence, then that's something you could do. Otherwise the biological and technical dif…

Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k

I can reproduce this and have opened an issue on the code base https://github.com/Bioconductor/support.bioconductor.org/issues/112

Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k

we can investigate this issue. thank you for bringing it to our attention

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Bioconductor 3.22 Released!

Comment: "Watched Tags" are being erased rather than updated

Comment: deseq2 filter the low counts

Answer: DESeq2 interactions

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