Tag: DRIMseq

I am having difficulty understanding the comparison between conditions in the design formula created for an analysis with DRIMSeq. Basically, I have 3 conditions: Healthy, Not_healthy1, Not_healthy2. My purpose is to feed the model comparing Healthy vs Not_healthy1 and Healthy vs Not_healthy2 (separately), but I am confused about the design…

1. Install r-bioc-drimseq package This guide let you learn how to install r-bioc-drimseq package: sudo apt install r-bioc-drimseq Copy 2. Uninstall / Remove r-bioc-drimseq package Please follow the guidance below to uninstall r-bioc-drimseq package: sudo apt remove r-bioc-drimseq Copy sudo apt autoclean && sudo apt autoremove Copy 3. Details of…

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA256 Format: 1.8 Date: Fri, 21 Jul 2023 17:35:20 +0200 Source: r-bioc-drimseq Architecture: source Version: 1.28.0-1 Distribution: unstable Urgency: medium Maintainer: Debian R Packages Maintainers <r-pkg-t…@alioth-lists.debian.net> Changed-By: Andreas Tille <ti…@debian.org> Changes: r-bioc-drimseq (1.28.0-1) unstable; urgency=medium . * Team upload. * New upstream version * Standards-Version:…

IsoformSwitchAnalyzeR Error in reading GTF file 0 Hi, I am using IsoformSwitchAnalyzeR v1.21.0 in R 4.3.0 environment using RStudio (2023.06.0+421 “Mountain Hydrangea” Release). When I try to import GTF file (obtained from Ensembl Plants) I get the following error ; Step 1 of 7: Checking data… Step 2 of 7:…

This is the development version of GenomicRanges; for the stable release version, see GenomicRanges. The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges package defines general purpose containers for storing…

DRIMseq error for paired sample analysis 0 @lucapiacentini-9597 Last seen 8 hours ago Italy Hello, I am doing a DTU with DRIMseq and I can get the results according to the following model: design_full <- model.matrix(~condition, data=DRIMSeq::samples(d)) where “condition” is my variable of interest (factor with 4 levels) and executing…

Hi, I am attempting to work through the workflow described in “Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification.” I am running into an error message when I try to make the counts dataframe for DRIMseq: Error in data.frame(gene_id = txdf$GENEID, feature_id = txdf$TXNAME, cts) : arguments…

DOI: 10.18129/B9.bioc.rnaseqDTU     This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see rnaseqDTU. RNA-seq workflow for differential transcript usage following Salmon quantification Bioconductor version: 3.14 RNA-seq workflow for differential transcript usage (DTU) following Salmon quantification. This workflow uses Bioconductor packages tximport, DRIMSeq, and…

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…

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…

—–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…

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…

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…