DEXSeq specifications


Unique identifier OMICS_01329
Name DEXSeq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.20.1
Stability Stable
Requirements BiocParallel, Biobase, SummarizedExperiment, IRanges, GenomicRanges, DESeq2, AnnotationDbi, RColorBrewer, S4Vectors, BiocGenerics, biomaRt, hwriter, Methods, tringr, Rsamtools, statmod, GenePlotter, GeneFilter
Maintained Yes



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DEXSeq article

DEXSeq citations

PMCID: 5884645

[…] at four different time points. raw reads were aligned to the ucsc mouse reference genome (mm10) using hisat2, and aligned reads were summarized at the gene or exon level using htseq. deseq2 and dexseq were used to model the gene and exon counts and test for differential expression and relative exon usage, respectively. after applying the appropriate transformation, gene counts were used […]

PMCID: 5499736

[…] in δupf1a (p-value = 0.0003564). as another major group of nmd targets is generated by as, we also searched for ptc-bearing transcripts derived from as isoforms. using the cufflinks toolkit, the dexseq algorithm, and manual validation with igv, we identified 274 nmd-sensitive transcripts generated by as. among these, 25 isoforms harbor a putative uorf (supplementary table s8). detailed […]

PMCID: 4777130

[…] were computed using the python package htseq (anders et al. 2015) (version 0.6.1p1) using the flybase annotation version r5.57 (st pierre et al. 2014). exon level counts were analyzed using the dexseq r package (anders et al. 2012, version 1.12.1). exon level ecdysone exposure effects are reported only for a model fit across all cell lines. thus, exon p-values and fold changes […]

PMCID: 5008907

[…] samples and 22,610,210 and 28,651,178 of 125 bp reads pairs for lacz samples were sequenced, respectively. the transcription analysis was performed using cufflinks (v2.2.1) (trapnell et al., 2012). dexseq was used to plot the transcripts to each gene (anders et al., 2012). rpkm method (reads per kilobase of transcript per million mapped sequence reads; mortazavi et al., 2008) was used […]

PMCID: 4664754

[…] the quartiles and overall range were consistent between biological replicates, indicating that the data were reproducible and of high quality., alternative splicing events were identified using the dexseq (v1.10.6) package, which models the exon counts as the negative binomial distribution and uses generalized linear models to test differential exon-usage using variance estimated […]

DEXSeq institution(s)
European Molecular Biology Laboratory, Heidelberg, Germany

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