Tag: DRIMseq

Separate exogenous from endogenous transcripts using Salmon RNAseq DTU

Dear friends, We are trying to use Salmon for DTU analysis. We want to separate exogenous from endogenous transcripts by following this post www.biostars.org/p/443701/ and this paper f1000research.com/articles/7-952 We are focusing on a gene called ASCL1 (endo-ASCL1). We transduced cells with lentiviral vector containing ASCL1 ORF only (Lenti-ASCL1). There should…

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Bioconductor – GeuvadisTranscriptExpr

DOI: 10.18129/B9.bioc.GeuvadisTranscriptExpr     This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see GeuvadisTranscriptExpr. Data package with transcript expression and bi-allelic genotypes from the GEUVADIS project Bioconductor version: 3.8 Provides transcript expression and bi-allelic genotypes corresponding to the chromosome 19 for CEU individuals from…

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Accepted r-bioc-drimseq 1.22.0-1 (source all) into unstable, unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Thu, 18 Nov 2021 21:20:39 +0100 Source: r-bioc-drimseq Binary: r-bioc-drimseq Architecture: source all Version: 1.22.0-1 Distribution: unstable Urgency: medium Maintainer: Debian R Packages Maintainers <r-pkg-t…@alioth-lists.debian.net> Changed-By: Steffen Moeller <moel…@debian.org> Description: r-bioc-drimseq – Differential transcript usage and tuQTL analyses with Changes: r-bioc-drimseq…

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DRIMSeq with more than 2 categories in the group

Good evening, I’d like to perform a DRIMSeq analysis with more than 2 categories in the group. Later I considered two categories (control and sick): n.small<-min(table(DRIMSeq::samples(d)$condition)) #How many samples are in the smallest group n.big<-max(table(DRIMSeq::samples(d)$condition)) #How many samples are in the largest group n <- n.small+n.big #Since we have 2…

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Bioconductor Forum

James W. MacDonald 57k 1 week, 5 days ago United States Answer: Biomart’s getBM returns no genes for an existing GO-term in grch38, and less the Michael Love 33k 1 week, 6 days ago United States Answer: Normalizing 5′ Nascent RNA-seq data to identify differentially expressed transcr Kevin Blighe 3.3k 2 weeks, 2 days ago Republic…

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