GENE-counter statistics

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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


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  • person_outline Jeff Chang <>

Publication for GENE-counter

GENE-counter in publications

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 […]

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 […]

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 […]

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 […]

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. […]

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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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