DEGseq statistics

info info

Citations per year

Number of citations per year for the bioinformatics software tool DEGseq
info

Tool usage distribution map

This map represents all the scientific publications referring to DEGseq per scientific context
info info

Associated diseases

This word cloud represents DEGseq usage per disease context
info

Popular tool citations

chevron_left Normalization Differential expression Alternative splicing events identification chevron_right
Want to access the full stats & trends on this tool?

Protocols

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, methods, stats, graphics, utils, ShortRead, grDevices, R(>=2.8.0), samr
Maintained Yes

Download


download.png
galaxy.png

Versioning


No version available

Documentation


Maintainers


  • person_outline Xuegong Zhang
  • person_outline Likun Wang
  • person_outline Xiaowo Wang

Publication for DEGseq

DEGseq citations

 (321)
library_books

RNA Seq profiling of circular RNAs in human laryngeal squamous cell carcinomas

2018
Mol Cancer
PMCID: 5930968
PMID: 29716593
DOI: 10.1186/s12943-018-0833-x

[…] ion mapped reads, including TopHat mapping and TopHat-Fusion mapping) [] was employed to calculate the expression level of individual circRNA. Differential expression between circRNAs was assessed by DEGseq algorithm. We defined the statistical criteria for selecting aberrant-expressed circRNA using a q-value < 0.05 with a fold change > 2.0 or < 0.5. […]

library_books

Maser: one stop platform for NGS big data from analysis to visualization

2018
PMCID: 5905357
PMID: 29688385
DOI: 10.1093/database/bay027

[…] es the abundance of each transcript to test differentially expressed genes (DEGs), and visualizes the resultant outputs with the Cufflinks suite (). The latter pipeline, ‘Trinity, Bowtie, eXpress and DEGseq’, subsequently maps raw NGS reads to transcriptome assembly using Bowtie () to estimate the abundance of transcriptome using eXpress () and test DEGs with DEGseq (). In both pipelines, the resu […]

library_books

RNA seq analysis of lncRNA controlled developmental gene expression during puberty in goat and rat

2018
BMC Genet
PMCID: 5879571
PMID: 29609543
DOI: 10.1186/s12863-018-0608-9

[…] Further analysis of RNA-seq data was performed using the statistical R package (ggplot2, DESeq, edgeR, and DEGSeq; R, Auckland, NZL), as well graphical representations, adopting multiple testing. SPSS 17.0 software package (SPSS, Chicago, IL, USA) was applied to analyze the qRT-PCR data. Significance of da […]

library_books

Identification of transcriptome signature for predicting clinical response to bevacizumab in recurrent glioblastoma

2018
PMCID: 5943425
PMID: 29573206
DOI: 10.1002/cam4.1439

[…] ere summarized into BED files using SAMtools and bedTools (bamToBed version 2.16.2) . The BED files were used to estimate reads per kilobase of transcript per million reads (RPKM) using the R package DEGseq . DEGseq: Differentially expressed genes were identified using the R package “DEGseq” . Samples were divided into two groups according to clinical response to bevacizumab.ssGSEA: Single‐sample […]

call_split

Transcriptomic Profiles of Brain Provide Insights into Molecular Mechanism of Feed Conversion Efficiency in Crucian Carp (Carassius auratus)

2018
Int J Mol Sci
PMCID: 5877719
PMID: 29538345
DOI: 10.3390/ijms19030858
call_split See protocol

[…] t per kilobase of exon model per million mapped reads (FPKM) for each unigene between the two groups (Low_vs_High). Differentially expressed genes (DEGs) between the two groups were identified by the DEGseq package (samples with three biological replicates) applying the MA-plot-based method with Random Sampling model (MARS) method. In this study, DEGs with significant expression abundance between […]

call_split

c di GMP Regulates Various Phenotypes and Insecticidal Activity of Gram Positive Bacillus thuringiensis

2018
Front Microbiol
PMCID: 5816809
PMID: 29487570
DOI: 10.3389/fmicb.2018.00045
call_split See protocol

[…] e number of reads mapped to each gene was recorded by R (Mortazavi et al., ) 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., ). We used FDR ≤0.001 and a ≥1.5-fold change (|log1.5 (Fold change) normalized| ≥1) as the threshol […]


Want to access the full list of citations?
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.

DEGseq reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review DEGseq