DEGseq pipeline

DEGseq specifications

Information


Unique identifier OMICS_01305
Name DEGseq
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 1.2.2
Stability Stable
Requirements qvalue, ShortRead, samr, methods
Maintained Yes

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Maintainers


  • person_outline Xuegong Zhang <>
  • person_outline Likun Wang <>
  • person_outline Xiaowo Wang <>

Publication for DEGseq

DEGseq IN pipelines

 (65)
2018
PMCID: 5758489
PMID: 29313259
DOI: 10.1186/s13568-017-0529-4

[…] ne expression levels were used for direct comparison among samples. expression values were standardized across the dataset to enable the data from different genes to be combined., using the r package degseq, degs were identified with a random sampling model on the basis of the read count for each gene at different developmental stages. false discovery rate ≤ 0.05 and absolute value of |log2ratio|  […]

2018
PMCID: 5776778
PMID: 29357938
DOI: 10.1186/s12958-017-0319-5

[…] counts of each gene were counted by htseq (v0.6.0) [36], and the reads per kilobase of one gene per million reads (rpkm) were calculated to estimate the expression level of genes in each sample. degseq (v1.18.0) [33] was used to analyze differentially expressed genes (degs) with parameters of fdr < 0.05 and |log2fc| ≥ 1., the mirna and mrna expression profiles were analyzed by magia2 […]

2018
PMCID: 5791383
PMID: 29434612
DOI: 10.3389/fpls.2018.00034

[…] v2.0.12. the number of reads for each gene in the samples was counted by htseq v0.6.0. the expression levels of the genes in each sample were estimated as reads per kilobase million mapped reads. degseq v1.14.0 software was used to identify the degs between two biological replicate samples using a model based on negative binomial distribution (wang et al., 2010). a p-value was assigned […]

2018
PMCID: 5793189
PMID: 29342957
DOI: 10.3390/genes9010038

[…] of the unigenes in each tissue sample was calculated and normalized using the fpkm (fragments per kilobase million) method [27]. differentially expressed gene (deg) analysis was performed using the degseq r package with a threshold of |log2 (fold change)| > 1 and corrected p-value < 0.05 [28]. go enrichment analysis was performed by mapping the degs to the go database and the gene numbers […]

2018
PMCID: 5816809
PMID: 29487570
DOI: 10.3389/fmicb.2018.00045

[…] of reads mapped to each gene was recorded by r (mortazavi et al., 2008) and normalized into rpkm (reads per kilo bases per million reads). the differentially expressed genes were recorded by the degseq package using the mars (ma-plot-based method with random sampling model) method (wang et al., 2010). we used fdr ≤0.001 and a ≥1.5-fold change (|log1.5 (fold change) normalized| ≥1) […]

DEGseq institution(s)
MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST/Department of Automation, Tsinghua, University, Beijing, China
DEGseq funding source(s)
Supported by National Natural Science Foundation of China (grant numbers 30625012, 60721003, 60905013); the National Basic Research Program of China (2004CB518605); Open Research Fund of State Key Laboratory of Bioelectronics, Southeast University of China.

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