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http://r-forge.r-project.org/projects/sequgio/
An algorithm to estimate isoforms expression from RNA-seq data based on a model that doesn''t assume uniform distribution of count within transcripts.
Proper citation: Sequgio (RRID:SCR_008867) Copy
http://lrcv-crp-sante.s3-website-us-east-1.amazonaws.com/
A gene set analysis algorithm for biomarker identification in the cloud.
Proper citation: YunBe (RRID:SCR_008740) Copy
http://bioinformatics.fccc.edu/software/OpenSource/FGDP/FGDP.shtml
A Java-based, Microarray or Genechip data analysis system.
Proper citation: FGDP (RRID:SCR_008910) Copy
http://www.biomedcentral.com/1471-2105/14/357/abstract
Sample size calculation based on exact test for assessing differential expression analysis in RNA-seq data. R code is available from the corresponding author.
Proper citation: A sample size calculation method (RRID:SCR_009469) Copy
http://www.cibiv.at/~niko/ngc/
A compressor for aligned HTS sequencing data that enables the complete lossless and lossy compression of mapped alignment data stored in SAM/BAM files.
Proper citation: NGC (RRID:SCR_009342) Copy
http://geckoe.sourceforge.net/
A complete, high-capacity centralized gene expression analysis system, developed in response to the needs of a distributed user community.
Proper citation: Gecko (RRID:SCR_009001) Copy
http://homes.cs.washington.edu/~dcjones/quip/
Compresses next-generation sequencing data in the FASTQ and SAM/BAM formats with extreme prejudice.
Proper citation: Quip (RRID:SCR_009362) Copy
http://bioinformatics.ua.pt/software/mfcompress/
A compression tool for FASTA and multi-FASTA files.
Proper citation: MFCompress (RRID:SCR_009301) Copy
http://bioinformatics.research.nicta.com.au/software/rlz/
Optimized relative Lempel-Ziv compression of genomes.
Proper citation: RLZ (RRID:SCR_009420) Copy
http://ftp://ftp.ieeta.pt/~ap/codecs/GReEn1.tar.gz
A compression tool recently proposed for compressing genome resequencing data using a reference genome sequence., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: GReEn (RRID:SCR_009264) Copy
http://omicslab.genetics.ac.cn/ISRNA/
An online toolkit for analyzing high-throughput small RNA sequencing data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: ISRNA (RRID:SCR_009565) Copy
http://users-mb.au.dk/pmgrp/downloads.php
A pipeline for small RNA-seq data analysis.
Proper citation: shortran (RRID:SCR_009636) Copy
http://scalce.sourceforge.net/Home
A FASTQ compression tool that uses locally consistent parsing to obtain better compression rate.
Proper citation: SCALCE (RRID:SCR_009658) Copy
http://www.labmedmolge.unisa.it/inglese/research/imir
A modular pipeline for comprehensive analysis of smallRNA-Seq data, comprising specific tools for adapter trimming, quality filtering, DE analysis, target prediction by integrating multiple open source modules and resources in an automated workflow.
Proper citation: iMir (RRID:SCR_009496) Copy
http://www.stanford.edu/group/wonglab/SpliceMap/
A de novo splice junction discovery and alignment tool.
Proper citation: SpliceMap (RRID:SCR_009650) Copy
http://www.allseq.com/default.aspx
Free online tools to find the best Sequencing Service provider for your project.
Proper citation: AllSeq (RRID:SCR_010053) Copy
http://dna.engr.uconn.edu/?page_id=105
Software package that can be used to infer isoform and gene expression levels from high-throughput transcriptome sequencing (RNA-Seq) data.
Proper citation: IsoEM (RRID:SCR_009993) Copy
http://code.google.com/p/bitseq/
A software application for inferring expression levels of individual transcripts from sequencing (RNA-Seq) data and estimating differential expression (DE) between conditions.
Proper citation: BitSeq (RRID:SCR_009904) Copy
http://bioen-compbio.bioen.illinois.edu/TrueSight/
Self-training Algorithm for Splice Junction Detection using RNA-seq.
Proper citation: TrueSight (RRID:SCR_009835) Copy
http://hkbic.cuhk.edu.hk/software/abmapper
A portable, easy-to-use package for spliced alignment, junction site detection, and reads mapping. The core module was written in C++ and wrapped in PERL scripts.
Proper citation: ABMapper (RRID:SCR_010242) Copy
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