DESeq protocols

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DESeq specifications

Information


Unique identifier OMICS_01306
Name DESeq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 1.20.0
Stability Stable
Requirements
methods, RColorBrewer, Biobase, IRanges, GenomicRanges, testthat, locfit, ggplot2, BiocParallel, S4Vectors(>=0.9.25), rmarkdown, knitr, genefilter, vsn, SummarizedExperiment(>=1.1.6), Hmisc, BiocGenerics(>=0.7.5), geneplotter, Rcpp(>=0.11.0), pheatmap, IHW, apeglm, ashr, tximport, tximportData, readr, pbapply, airway, pasilla(>=0.2.10)
Maintained Yes

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Maintainers


  • person_outline Michael Love <>
  • person_outline Simon Anders <>

Additional information


An implementation for detection of differential translated genes using Ribo-seq is available at https://github.com/SGDDNB/DTG-detection

Publication for DESeq

DESeq in pipelines

 (738)
2018
PMCID: 5758812
PMID: 29311649
DOI: 10.1038/s41598-017-17878-x

[…] only uniquely mapped reads determined the number of reads per gene (htseq-count script 0.6.1p1). differentially expressed genes, were determined by padj < 0.05 and an absolute fold change >2 (deseq. 2 package v1.4.5) and hierarchical clustering using pearson dissimilarity and complete linkage was performed to explore gene expression patterns (matlab 8.0.0.783)., analysis was performed […]

2018
PMCID: 5761711
PMID: 29295970
DOI: 10.12659/MSM.905410

[…] we identified the significant demrnas and demirnas in gastric cancer samples compared with the normal samples. a total of 2024 differentially expressed mrnas and 198 mirnas were identified by the “deseq” package in r. then, the heat map with complete linkage clustering of demrnas and demirnas was built using the “gplots” package in r. (, ). as a result, there were 1042 (51.48%) up-regulated […]

2018
PMCID: 5761873
PMID: 29320577
DOI: 10.1371/journal.pone.0190485

[…] individual annotation track files used for predicting the genomic origin of the pirnas were downloaded from ucsc ftp site., the differential expression analysis of the small rnas was performed using deseq of bioconductor [] to obtain a set of pirnas significantly up- or down-regulated in each of the two eoca types with respect to normal ovary as a control. the expression levels (up/down) […]

2018
PMCID: 5761878
PMID: 29320569
DOI: 10.1371/journal.pone.0190175

[…] the correlation coefficients (r2) between replicates were calculated using pearson correlation. subsequently, the differential expression detection of genes across libraries was analyzed using the deseq r package (1.10.1) []. the p values were adjusted using the benjamini and hochberg method []. an adjusted p value (padj) <0.05 found by deseq and |log (fold change)| >1 constituted […]

2018
PMCID: 5768636
PMID: 29375320
DOI: 10.3389/fncel.2017.00434

[…] mapped reads (fpkm) value of each gene was calculated and normalized using cufflinks (). the read counts of genes in the two groups were obtained using htseq-count (). degs were identified using the deseq functional estimator sizefactors and nbinomtest (). multiple-test-corrected p-value < 0.05 and absolute fold change > 2 were set as the thresholds for screening significantly […]


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DESeq in publications

 (2395)
PMCID: 5958101
PMID: 29773797
DOI: 10.1038/s41467-018-04364-9

[…] by standard illumina methods. tophat2 was used to map quality-filtered reads onto the s. schorii draft genome. differential gene expression was then analysed with readxplorer 2.0 including the deseq package. the results (fig. ) clearly show that genes from asl7 to asr7, inclusive, are significantly upregulated under producing conditions, while genes outwith this area show no significant […]

PMCID: 5955945
PMID: 29769567
DOI: 10.1038/s41598-018-25800-2

[…] of a maximum read count >20 across all samples. read counts were normalized by the trimmed mean of m-values normalization method. the differentially expressed genes were identified using the deseq r package (www-huber.embl.de/users/anders/deseq/). gene set enrichment tests were performed using the gage r tool. clustering was performed by principal component analysis and hierarchical […]

PMCID: 5955949
PMID: 29769539
DOI: 10.1038/s41598-018-25743-8

[…] by reads per kilobase per million mapped reads. hierarchical clustering of representative mrnas and mirnas expressions was performed to reveal reproducibility in biological replicates., the deseq package was used to detect degs and dems between the normal and nafld groups, with thresholds of a two-fold change (the ratio between seven nafld rats’ and seven normal rats’ averaged signal […]

PMCID: 5954139
PMID: 29765020
DOI: 10.1038/s41467-018-04295-5

[…] random variable, and we estimated the relationship between the mean and variance by grouping pairs of loci that are separated by the same linear genomic distance. we adapted the model employed by deseq to hi-c data by using an explicit specific scaling factor corresponding to bin-specific ice biases. in addition, we estimated variance and dispersion of the negative binomial without replicates […]

PMCID: 5954018
PMID: 29765063
DOI: 10.1038/s41598-018-25702-3

[…] qualified rna sequencing data were mapped to the mouse genome (grcm38/mm10) and annotated using tophat software. the expression levels of lncrnas and mrnas were normalized and tested using deseq software. lncrnas or mrnas with fold change >2 and padj (value adjusted for multiple testing with the benjamini-hochberg procedure) <0.05 were defined as significantly differential […]


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DESeq institution(s)
Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA; Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA; Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany; Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
DESeq funding source(s)
Supported by a stipend from the International Max Planck Research School for Computational Biology and Scientific Computing, a grant from the National Institutes of Health (5T32CA009337-33), and the European Union’s 7th Framework Programme (Health) via Project Radiant.

DESeq reviews

 (5)
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Anamaria Elek's avatar image No country

Anamaria Elek

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DESeq2 package in R is a first-choice for DE analysis

Thyago

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DEseq2 is a very robust and fast package for differential gene expression analysis of RNA-seq data. It has a very intuitive pipeline to get most out of your data with few lines of code. The documentation is also pretty straightforward, I would only include more Case Studies, since the technique is used with many diverse experimental designs. On the other hand, Bioconductor mailing list and forums frequented by the author(s) help circuvemting this. In summary, is a must tool for a bioinformatician toolkit.