FX is a user-Frendly RNA-Seq gene eXpression analysis tool, empowered by the concept of cloud-computing. With FX, you can simply upload your RNA-Seq raw FASTQ data on the cloud, and let the computing infra to do the heavy analysis.
Bioinformatics. 2012 Mar 1;28(5):721-3. doi: 10.1093/bioinformatics/bts023. Epub 2012 Jan 17. FX: an RNA-Seq analysis tool on the cloud.
Hong D1, Rhie A, Park SS, Lee J, Ju YS, Kim S, Yu SB, Bleazard T, Park HS, Rhee H, Chong H, Yang KS, Lee YS, Kim IH, Lee JS, Kim JI, Seo JS.
EMSAR (Estimation by Mappability-based Segmentation And Reclustering) is a new approach for quantifying transcript abundance from RNA-seq data.The software groups reads according to the set of transcripts to which they are mapped and finds maximum likelihood estimates using a joint Poisson model for each optimal set of segments of transcripts.
ArrayExpressHTS is an R and Bioconductor RNA-seq processing pipeline that highly utilizes distributed computing for data processing and quality assessment of High-Throughput Sequencing experiments and datasets
RNASeqMut is an easy-to-use program to detection variants in RNA-Seq read alignments. rnaseqmut is a light-weight C++ program to detect variants (or mutations, including SNPs, indels, RNA editing events) from a single or multiple RNA-Seq BAM files.