DEGseq specifications

Information


Unique identifier OMICS_01305
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 <>

DEGseq article

DEGseq citations

 (16)
2018
PMCID: 5796109

[…] one method was used to accurately assess gene expression level [35]., differential expression analysis of genes across samples with biological replicates was performed using the package degseq [88]. degseq provided statistical method for deciding differential expression genes; the resultant p-values were adjusted employing the reported methods for limiting the false discovery rate [89]. genes […]

2017
PMCID: 5722506

[…] were calculated., based on rna sequencing, gene expression levels were measured as the number of reads per kb of exon regions per million mapped reads (rpkm). degs were detected with the r package degseq software. a corrected p-value of 0.05 and a |log2 (fold change)| of 1 were set as the threshold for statistically significant differential expression. for the genes that were differentially […]

2017
PMCID: 5510844

[…] were amplified with three biological replications and with three technical replication each biological replication., differential expression analysis of two conditions was performed using the degseq r package (1.20.0) [33]. p values were adjusted using the benjamini–hochberg method. corrected p-values of 0.005 and a log2 (fold-change) of 1 were set as the threshold for significant […]

2017
PMCID: 5424160

[…] was sequenced by novogene (beijing, china) using the illumina hiseq4000 platform. reads were alligned to the human genome hg19 with bowtie v2.2.3. gene expression analysis was performed using the degseq r package (1.26.0). unsupervised clustering was performed using cluster and tree view and visualized using heat maps. enrichment pathway analysis of genes was compiled from biocarta and kyoto […]

2017
PMCID: 5394545

[…] method to estimate the level of gene expression51. the gene-level rpkm values were then normalized using the log10 values (rpkm + 1) for further analyses. differential expression was determined with degseq software, and the q-value was used to denote the significance of the p-value (q-value < 0.05 is recommended)52. the data were deposited in gene expression omnibus (geo) with accession […]

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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