DiffSplice 0.1.2beta – Discover Alternative Splicing Variants present in an RNA-seq dataset

DiffSplice 0.1.2beta

:: DESCRIPTION

DiffSplice is a novel tool for discovering and quantitating alternative splicing variants present in an RNA-seq dataset, without relying on annotated transcriptome or pre-determined splice pattern. For two groups of samples, DiffSplice further utilizes a non-parametric permutation test to identify significant differences in expression at both gene level and transcription level. DiffSplice takes as input the SAM files that supply the alignment of the RNA-seq reads on the reference genome, obtained from an RNA-seq aligner like MapSplice. The results of DiffSplice are summarized as a decomposition of the genome and can be visualized using the UCSC genome browser.

::DEVELOPER

Bioinformatics Lab @CS.UKy.edu

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

 DiffSplice

:: MORE INFORMATION

Nucleic Acids Res. 2013 Jan;41(2):e39. doi: 10.1093/nar/gks1026. Epub 2012 Nov 15.
DiffSplice: the genome-wide detection of differential splicing events with RNA-seq.
Hu Y, Huang Y, Du Y, Orellana CF, Singh D, Johnson AR, Monroy A, Kuan PF, Hammond SM, Makowski L, Randell SH, Chiang DY, Hayes DN, Jones C, Liu Y, Prins JF, Liu J.

RegTools 0.5.2 – Integrated analysis of Genomic and Transcriptomic data for discovery of Splicing Variants in Cancer

RegTools 0.5.2

:: DESCRIPTION

RegTools is a set of tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context.

::DEVELOPER

The Griffith Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • Python

:: DOWNLOAD

RegTools

:: MORE INFORMATION

Citation

RegTools: Integrated analysis of genomic and transcriptomic data for discovery of splicing variants in cancer
Yang-Yang Feng, et al.
doi: https://doi.org/10.1101/436634