Open Source RNA-Seq Data Analysis Tools from Google Project Hosting

est2assembly  –  Assembly and annotation of transcriptomes for any species
Activity: Medium  –  Updated: Earlier this year  –  Stars: 3
The est2assembly platform is the only platform for standardising transcriptome projects: go from raw trace files to an annotated GBrowse interface driven by the Seqfeature database. It accepts both Sa…

 altanalyze  –  Alternative splicing and functional prediction analysis tool
Activity: High  –  Updated: Yesterday  –  Stars: 3
AltAnalyze is a freely available, open-source and cross-platform program that allows you to take RNASeq or relatively raw microarray data (CEL files or normalized), identify predicted alternative splicing…

ibm-cbc-genomic-tools  –  GenomicTools: a computational platform for developing high-throughput …
Activity: High  –  Updated: Last 30 days
Contents GenomicTools is a flexible computational platform for the analysis and manipulation of high-throughput sequencing data such as RNA-Seq…

 iqseq  –  Integrated Isoform Quantification Analysis based on A Partial Sampling …
Activity: Medium  –  Updated: Earlier this year
IQSeq is a tool for isoform quantification with RNA-seq data. Given isoform annotation and alignment of RNA-seq reads, it will use EM algorithm to infer the most probable expression level for each…

 chimerascan  –  Detection of chimeric transcripts in high-throughput sequencing data
Activity: High  –  Updated: Last 7 days  –  Stars: 1
Chimerascan version 0.4.3 (released Aug 2, 2011) includes a number of improvements and is recommended for all users Support for compressed FASTQ files (gzip, bzip2, and ZIP) A new module…

 comrad  –  Discovery of gene fusions using paired end RNA-Seq and WGSS
Activity: Medium  –  Updated: Earlier this year
Both paired end whole transcriptome shotgun sequencing (RNA-Seq), and paired end Whole Genome Shotgun Sequencing (WGSS), can be used to discover rearrangements in tumour genomes. Comrad is a novel…

 jagn  –  A Java-Based Model for Artificial Gene Networks Generation
Activity: Medium  –  Updated: Earlier this year  –  Stars: 1
In a biological context, the cells can be viewed as networks of molecules connected by chemical reactions. The development of massive data collection techniques, as cDNA microarrays and RNA-Seq…

 ever-seq  –  Evaluate Experiment of RNA-seq
Activity: None  –  Updated: Today
Deep transcriptome sequencing (RNA-seq) provides massive and valuable information about functional elements in the genome. Using RNA-seq data, people can profile gene (and allele specific)…

 rna-seq-calfs  –  Calculate genes’ Fragmental Splicing level using RNA-seq
Activity: Medium  –  Updated: Last 7 days
Through large scale meta analyses of clinical RNA-seq data, we found that disease samples usually have much higher level of fragmental splicings (kind of aberrant splicing) compared with (matched)…

 tbrowse  –  HTML5 Transcriptome Browser
Activity: None  –  Updated: May 23, 2010  –  Stars: 9
tbrowse is HTML5/javascript based browser designed specifically for visualizing RNA-seq results. This project aims to provide a simple, intuitive browser for exploring RNA-seq data in the familiar …

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