Bioconductor GenomeIntervals

Showing : genomeIntervals • reset

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genomeIntervals GenomicRanges

22 months ago gshweta95 • 0

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granges bed genomicranges genomeintervals deseq2

8.0 years ago rbronste ▴ 60

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genomeintervals UTRs exons CDS GenomicRanges

updated 8.5 years ago by Michael Lawrence ★ 11k • written 8.5 years ago by rubi ▴ 110

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nclist genomeintervals

updated 10.0 years ago by Hervé Pagès 16k • written 10.0 years ago by Jurat Shahidin ▴ 80

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genomeIntervals

updated 10.6 years ago by Nicolas Delhomme ▴ 320 • written 10.8 years ago by mhz • 0

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genomeintervals

updated 10.6 years ago by Nicolas Delhomme ▴ 320 • written 10.6 years ago by sjackman • 0

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BSgenome hexbin BSgenome IRanges genomeIntervals GenomicRanges girafe Rsamtools HiTC HiTC

updated 12.9 years ago by Dan Tenenbaum ★ 8.2k • written 12.9 years ago by Wim Kreinen ▴ 100

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Annotation convert genomeIntervals Annotation convert genomeIntervals

13.9 years ago delhomme@embl.de ★ 1.2k

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genomeIntervals genomeIntervals

updated 14.8 years ago by Hervé Pagès 16k • written 14.8 years ago by Julien Gagneur ▴ 50

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Sequencing Annotation GO rtracklayer IRanges genomeIntervals Sequencing Annotation GO

16.0 years ago Robert Castelo ★ 3.4k

10 results • Page 1 of 1

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Comment: Combining two proteomics datasets with limpa by Andrew Pattison • 0

Thanks heaps Gordon. I went with option 1 and no normalisation and all seems to have worked well. Cheers, Andrew

Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k

Flagging protein groups as likely contaminants in this way will be fine for a limpa analysis. The `Cont_` proteins can optionally stay in f…

Answer: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Gordon Smyth 53k

Aaron Lun was a PhD student in my Lab back in 2015, when he posted the answers about allele-specific expression that you and Mike Love have…

Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Michael Love 43k

You just need the mouse identifier (controls baseline) and the group specific allelic effect.

Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Julia Broadbent • 0

Hi Emily, Just sharing a resource for handling contaminants - we use the methods described in [Frankenfield et al. (2022)](https://pubs.acs…

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A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen

Comment: limpa analysis advice

Answer: When to use edgeR or limma

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