Bioconductor GFF3

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dexseq python gtf gff3 annotation

5.7 years ago Raito92 ▴ 60

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2.8k

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annotation gff3 gff genome

updated 6.4 years ago by Michael Lawrence ★ 11k • written 6.4 years ago by mictadlo ▴ 10

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parclip bedtools bed files gff3

8.0 years ago linuxborg2 • 0

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txdb gff3 polycistronic transcript

8.2 years ago Piotr Gawronski • 0

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4.1k

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GenomicFeatures GFF3

updated 8.8 years ago by Valerie Obenchain ★ 6.8k • written 8.8 years ago by Dario Strbenac ★ 1.6k

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4.6k

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AnnotationHub Gencode GFF3 FASTA News

10.4 years ago Sonali Arora ▴ 390

6 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: DESeq2: Is it possible to convert read counts to expression values via TPM and r

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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