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GENE-counter specifications


Unique identifier OMICS_01404
Name GENE-counter
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++, Perl, R
Database management system MySQL
Computer skills Advanced
Stability Stable
Maintained Yes


No version available



  • person_outline Jeff Chang

Publication for GENE-counter

GENE-counter citations


Benzo[a]pyrene induced metabolic shift from glycolysis to pentose phosphate pathway in the human bladder cancer cell line RT4

Sci Rep
PMCID: 5575001
PMID: 28851999
DOI: 10.1038/s41598-017-09936-1

[…] overview about the involved pathways. following maldi-tof-ms analysis, the proteins were searched for their corresponding official gene name in the universal protein resource (uniprot) database. the gene counter parts were then uploaded to the stitch classification system software, which grouped the identified proteins into its respective protein pathways (fig. ). the analysis revealed […]


Contribution of the non effector members of the HrpL regulon, iaaL and matE, to the virulence of Pseudomonas syringae pv. tomato DC3000 in tomato plants

BMC Microbiol
PMCID: 4544800
PMID: 26285820
DOI: 10.1186/s12866-015-0503-8

[…] identify 5′-ends of transcripts in pto dc3000 grown in iron-limited mg medium, including those corresponding to the iaal gene [, ]. moreover, transcriptome profiling using rna-seq coupled with the gene-counter software package [] recently expanded characterization of the hrpl regulon from six p. syringae strains, including pto dc3000, and pointed again at the iaal and mate genes as members […]


Large Scale Transcriptome Analysis of Two Sugarcane Genotypes Contrasting for Lignin Content

PLoS One
PMCID: 4524650
PMID: 26241317
DOI: 10.1371/journal.pone.0134909

[…] transcripts, distribution of transcripts lengths, n50 value, and mainly the results of phylogenetic analysis of previously selected genes from lignin biosynthesis pathway, as described below. gene-counter software [] was used to quantify gene expression, in which reads from each library were mapped against the performed assembly. finally, the differential expression analysis […]


RNA Seq analysis of resistant and susceptible potato varieties during the early stages of potato virus Y infection

BMC Genomics
PMCID: 4475319
PMID: 26091899
DOI: 10.1186/s12864-015-1666-2

[…] 36.6 million. mapping to the potato dm genome [], transcript assembly, and quantification were performed by using two analytical pipelines: tophat and cufflinks [], or jeans, a modified version of gene-counter []. these two different pipelines use different short read aligners, bowtie (burrows-wheeler transformation) and cashx 2.3 [], respectively. the number of transcripts identified […]


RNA seq Analysis of Early Hepatic Response to Handling and Confinement Stress in Rainbow Trout

PLoS One
PMCID: 3928254
PMID: 24558395
DOI: 10.1371/journal.pone.0088492

[…] the count table. only reads mapped uniquely to a reference sequence or a newbler isogroup were included in the count table. we used the statistics package deseq incorporated in software package gene-counter to process the count table to identify dets. the count table was directly imported into the system and the “fit-only” option was selected for the dispersion estimation step of deseq. […]


Variable Suites of Non effector Genes Are Co regulated in the Type III Secretion Virulence Regulon across the Pseudomonas syringae Phylogeny

PLoS Pathog
PMCID: 3879358
PMID: 24391493
DOI: 10.1371/journal.ppat.1003807

[…] specifically informing studies of the hrpl regulon –., in this study, we defined the hrpl regulon of six distinct strains of p. syringae with complete or draft genomes using rna-seq coupled with the gene-counter software package –. we sought primarily to compare the diversity of non-t3e hrpl-regulated genes between strains and secondarily to determine if there were additional type iii effectors […]

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GENE-counter institution(s)
Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA; Molecular and Cellular Biology Program, Oregon State University, Corvallis, OR, USA; Department of Statistics, Oregon State University, Corvallis, OR, USA; Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, USA
GENE-counter funding source(s)
Supported in part by Oregon State University (OSU) and the National Research Initiative Competitive Grant no. 2008-35600-18783 from the USDA’s National Institute of Food and Agriculture, Microbial Functional Genomics Program, National Science Foundation (MCB-0618433) and National Institutes of Health (AI43288), and OSU and the Department of Energy’s Plant Feedstock Genomics for Bioenergy grant DE-FG02-08ER64630 and by Computational and Genome Biology Initiative Fellowships from OSU.

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