Software

Software tools developed and made available by the Chang lab

GENE-counter

genecounter GENE-counter is a computational pipeline for analyzing RNA-Sequencing (RNA-Seq) data for differential gene expression of eukaryotes, prokaryotes, as well as organisms with no available genome reference sequence. GENE-counter is a complete pipeline that automates the process of enumerating, aligning, and assigning sequences to generate count data to simplify high-throughput sequence analysis. To analyze data for differential gene expression, GENE-counter can be run with any one of three statistics packages that are based on variations of the negative binomial distribution. The default method is a new and simple statistical test we developed based on an over-parameterized version of the negative binomial distribution. GENE-counter also includes three different methods for assessing differentially expressed features for enriched gene ontology (GO) terms.

Note: Documentation for installing, configuring, and using GENE-counter is found in the 'DOCUMENTS' folder in the GENE-counter installation download below.

Please reference this paper.

For more information concerning the statistical package developed for GENE-counter please see: Di, Yanming; Schafer, Daniel W.; Cumbie, Jason S.; and Chang, Jeff H. (2011) "The NBP Negative Binomial Model for Assessing Differential Gene Expression from RNA-Seq," Statistical Applications in Genetics and Molecular Biology: Vol. 10: Iss. 1, Article 24.

Latest GENE-counter Version (v0.4.4) Mac/Linux:
GENE-counter

GENE-counter Data
Arabidopsis thaliana RNA-Seq data

Arabidopsis thaliana GENE-counter

reference sequence database data

GENE-counter database / sequence data
CASHX Database (Index Length:16nt / File Size: 1.8GB)

Genome analysis scripts

Download: scripts.zip

AutoSPOTs

autospots AutoSPOTs is a Graphical User Interface for the automated batch analysis of JPEG images for fluorescent spots. We developed AutoSPOTs for identifying and quantifying aniline-stained callose deposits. We have validated its use for studying Pseudomonas-infected leaves of Arabidopsis.

Please reference: J. S. Cumbie, R. C. Pankow, W. J. Thomas, and J. H. Chang (2010) AutoSPOTs: Automated Image Analysis for Enumerating Callose Deposition in 10th Japan-US Seminar: Genome-Enabled Integration of Research in Plant Pathogen Systems, K. Akimitsu, et al., Editors. 2010, APS press: St. Paul, MN.

Note for Mac users AutoSPOTs requires Perl 5.8.x. Snow Leopard users will need a separate installation of Perl since the OS-dependant installation comes with Perl 5.10.x. This version is incompatible with the Tk module needed to run AutoSPOTs. Mac users with the proper install of Perl can follow the instructions as described for the Linux 32-bit platform. We have not attempted to install AutoSPOTs on a Mac.

AutoSPOTs and its associated documents are available for download:

AutoSPOTs:
Download: AutoSPOTs.tar.gz

Install Documentation: Download

Manual: Download