EBSeq specifications

Information


Unique identifier OMICS_01307
Name EBSeq
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Input format CSV,XLS,XLSX
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 1.18.0
Stability Stable
Requirements blockmodeling, gplots, testthat
Maintained Yes

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Documentation


Maintainers


  • person_outline Christina Kendziorski <>
  • person_outline Ning Leng <>

Additional information


https://www.biostat.wisc.edu/~kendzior/EBSEQ/

EBSeq article

EBSeq citations

 (5)
2018
PMCID: 5855618

[…] function, which uses singular value decomposition, generally providing better numerical accuracy., to detect degs between b. dorsalis and b. correcta, we used the empirical bayes hierarchical model ebseq [72]. in this analysis, we adopted a well-established benjamini–hochberg method to calibrate p values from the original assumption test [73]. after calibration, the p value was determined using […]

2016
PMCID: 4925018

[…] 2011). expression data were estimated as log2(fpkm). the significance of the differential expression between the lacz and m5 phenotypes was estimated by using the ebseq method implemented in the ebseq r library (leng et al., 2013), based on the significance cutoff (p < 0.05) for the posterior probability. the rnaseq data for the mthfd2 kd experiment is available for download from geo […]

2016
PMCID: 5029680

[…] analysis. high quality reads were aligned against human transcriptome (hg19) using rsem package v1.2.21 [46]. expression estimation and tests for differential expression were performed using ebseq v1.6.0 in the rsem package [47]. transcriptome sequencing data available publicly at gene expression omnibus (http://www.ncbi.nlm.nih.gov/geo/) under accession number gse71993., rna sequencing […]

2015
PMCID: 4545301

[…] by rsem (v1.2.19) to estimate expression levels of all genes. the expression level of a gene is expressed as a gene-level fpkm (fragments per kilobase of transcripts per million mapped reads) value. ebseq (v1.5.4), as an integral component of rsem package, was used to identify differentially expressed genes. ucsc genes for mouse mm9 from igenome […]

2014
PMCID: 4148442

[…] accession number nc_007605.1) with a known transcriptome annotation [62]. we used the expectation-maximization (em) algorithm in rsem [57] with bowtie 2 [72] to estimate gene expression levels. ebseq within rsem pipeline was used to identify differentially expressed genes [56]., cells were harvested and re-suspended in 400 µl of lysis buffer containing 50 mm tris-hcl [ph 8.1], 1% sds, […]

EBSeq institution(s)
Department of Statistics, University of Wisconsin, Madison, WI, USA; Morgridge Institute for Research, Madison, WI, USA; McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin, Madison, WI, USA; Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, USA
EBSeq funding source(s)
Supported by NIH GM102756, NIH CA28954, NIEHS ES17400 and The Morgridge Institute for Research.

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