More Open Access RNA-Seq Analysis Software

GENE-counter is a complete Perl-based computational pipeline for analyzing RNA-Sequencing (RNA-Seq) data for differential gene expression. In addition to its use in studying transcriptomes of eukaryotic model organisms, GENE-counter is applicable for prokaryotes and non-model organisms without an available genome reference sequence. For alignments, GENE-counter is configured for CASHX, Bowtie, and BWA, but an end user can use any Sequence Alignment/Map (SAM)-compliant program of preference.

Cumbie JS, Kimbrel JA, Di Y, Schafer DW, Wilhelm LJ, Fox SE, Sullivan CM, Curzon AD, Carrington JC, Mockler TC, Chang JH. (2011) GENE-Counter: A Computational Pipeline for the Analysis of RNA-Seq Data for Gene Expression Differences. PLoS One 6(10), e25279. [article]


S-MART is a toolbox which handles mapped RNA-Seq data. S-MART is an intuitive and lightweight tool which performs many of the tasks usually required for the analysis of mapped RNA-Seq reads. S-MART does not require any computer science background and thus can be used by all of the biologist community through a graphical interface. S-MART can run on any personal computer, yielding results within an hour even for Gb of data for most queries. S-MART may perform the entire analysis of the mapped reads, without any need for other ad hoc scripts. With this tool, biologists can easily perform most of the analyses on their computer for their RNA-Seq data, from the mapped data to the discovery of important loci.

S-MART can be downloaded for free from, and can be used on any platform (Linux, Windows or Mac). S-MART has been developed under the CeCILL license, which is compatible with the GNU GPL license.

  • Zytnicki M, Quesneville H. (2011) S-MART, A Software Toolbox to Aid RNA-seq Data Analysis. PLoS One. 6(10), e25988. [article]