DEXSeq protocols

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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Publication for DEXSeq

DEXSeq IN pipelines

PMCID: 5276861
PMID: 28194146
DOI: 10.3389/fmicb.2017.00098

[…] to a reference sequence with tophat v2.0.9 and bowtie2 v2.1.0. gene abundances were derived by htseq. differential expression was estimated by pair-wise negative binomial tests with edger and dexseq. gene ontology (go) enrichment was performed by gtac-wustl. each gene was assigned a go category per the broad institute’s pfam annotations using the provided map1. any genes with a p < […]

PMCID: 5318384
PMID: 28270748
DOI: 10.3389/fncel.2017.00033

[…] expression using negative binomial generalized linear models implemented by the deseq2 r package (love et al., 2014). additionally, differential exon usage analysis was performed using the dexseq r package (anders et al., 2012). the rna-seq data has been deposited to the ncbi geo database with an accession number gse92905., we investigated potential role for wild type and mutant htt […]

PMCID: 5406905
PMID: 28446200
DOI: 10.1186/s12943-017-0653-4

[…] and counts per gene generated using htseq [40]. differential expression at both the gene and exon level was carried out in r ( using the ‘deseq’ and dexseq’ r packages [41]. the resulting p values were adjusted for multiple testing with benjamini and hochberg’s [42] method to control the false discovery rate. genes with a p value <0.05 […]

PMCID: 5499736
PMID: 28402567
DOI: 10.1093/nar/gkx256

[…] table s4) and novel transcripts were identified using the cufflinks toolkit (39). differential gene expression and exon expression (or usage) analyses were carried out using the cuffdiff and dexseq algorithms, respectively (40). the following criteria were used to identify transcripts upregulated in mutants: (i) the transcript fpkm (fragments per kilobase of exon per million fragments […]

PMCID: 5499736
PMID: 28402567
DOI: 10.1093/nar/gkx256

[…] 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 […]

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

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