2009
DOI: 10.1093/bioinformatics/btp612
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DEGseq: an R package for identifying differentially expressed genes from RNA-seq data

Abstract: The R package and a quick-start vignette is available at http://bioinfo.au.tsinghua.edu.cn/software/degseq

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Cited by 3,726 publications
(2,561 citation statements)
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References 11 publications
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“…Differentially expressed genes (DEGs) between two conditions/groups were analyzed using the DEGSeq R package (1.12.0) (http://bioinfo.au.tsinghua.edu. cn/software/degseq) 80 . The P values were adjusted using the BH method 81 .…”
Section: )mentioning
confidence: 99%
“…Differentially expressed genes (DEGs) between two conditions/groups were analyzed using the DEGSeq R package (1.12.0) (http://bioinfo.au.tsinghua.edu. cn/software/degseq) 80 . The P values were adjusted using the BH method 81 .…”
Section: )mentioning
confidence: 99%
“…Gene expression differences between cork and holm oak contigs with at least 10 mapped reads were statistically analysed, as has previously been done by Bourgis et al (2011), with DEGseq software using the MA-plot-based random sampling model (Wang et al 2009). To consider transcripts as differentially expressed (DE), we established a two-fold cut-off: log 2 fold-change (FC) (−1 ≤ log 2 FC ≥ 1) and statistical significance of q-value < 0.05 (p-value corrected for false discovery rate (Benjamini and Hochberg 1995)).…”
Section: Bioinformatics and Data Analysismentioning
confidence: 99%
“…The DEGseq package (Wang et al 2009) was used to identify differentially expressed contigs between cork oak and holm oak external bark libraries. The analysis identified 2600 DE contigs: 1030 contigs were cork oak upregulated and 1570 downregulated (Table S1).…”
Section: Differential Gene Expression Between Cork Oak and Holm Oak Omentioning
confidence: 99%
“…Gene ontology (GO) was predicted by WEGO (Web Gene Ontology) in terms of cellular component, molecular function, and biological process [29,30]. Differentially expressed genes were identified by the DEGseq package in R language [31]. To gain an overview of gene networks, KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways were analyzed by GenMAPP 2.1 [32][33][34][35][36].…”
Section: Gene Expression Analysismentioning
confidence: 99%