DEGseq protocols

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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

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Maintainers


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

Publication for DEGseq

DEGseq in pipelines

 (127)
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: 5771010
PMID: 29338737
DOI: 10.1186/s12985-018-0926-6

[…] sample. rpkm can eliminate the effect of sequencing depth and gene length on gene expression levels, which facilitates the comparison of the number of transcript levels generated between samples. degseq (v1.18.0) was used to identify differentially expressed genes (degs) between the viruliferous and nonviruliferous guts. genes with q ≤ 0.05 (adjusted p-value) and log2 ratio ≥ 1 […]

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

[…] read counts of each gene were counted by htseq (v0.6.0) [], 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) [] 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., ). 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 []. 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 []. go enrichment analysis was performed by mapping the degs to the go database and the gene numbers […]


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DEGseq in publications

 (512)
PMCID: 5941544
PMID: 29739311
DOI: 10.1186/s12864-018-4727-5

[…] []. to identify mirnas related to male abortion in 337s at the sl environmental condition, differential expression analysis of mirna fold changes between two samples was performed using the degseq r package and adjusted using q value []. the threshold level of q-value (< 0.01) and absolute value of log2ratio (≥1) were used to judge the significant difference of mirnas expression […]

PMCID: 5930780
PMID: 29720105
DOI: 10.1186/s12864-018-4706-x

[…] unigenes, we use hmmer [] to compare them with pfam database to get the annotation information of unigenes., edger program package was used for adjusting read counts of each sequenced library, and degseq (2010) r package was used for differential expression analysis of two samples. p value was adjusted using q value []. in this study, q value < 0.01 and |log2 (fold change)| > 1 were set […]

PMCID: 5919661
PMID: 29698526
DOI: 10.1371/journal.pone.0196537

[…] the read counts for each sequenced library were adjusted by the edger program package with one scaling normalization factor. genes differentially expressed between two samples were analyzed with the degseq (2010) r package. the p-value was adjusted using the q-value []. the following threshold was applied to identify differentially expressed genes: q-value < 0.005 and |log2 (fold change)| ≥ […]

PMCID: 5928209
PMID: 29740343
DOI: 10.3389/fphys.2018.00432

[…] were adjusted by edger 3.0.8 program package through one scaling normalized factor for each sequenced library. then, the differential expression analysis of two samples was performed using the degseq 1.12.0 r package (wang et al., ). p-value was adjusted using q-value (storey, ). q < 0.005 & |log2(foldchange)|>1 was set as the threshold for significantly differential expression., […]

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

[…] levels of genes as 2–δδct. expression levels were normalized to β-actin levels.table 1, 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 […]


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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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