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https://code.google.com/p/swdmr/
A free software using a sliding-window approach to identify differentially methylated regions (DMR) from whole-genome bisulfite sequencing.
Proper citation: swDMR (RRID:SCR_007316) Copy
http://web.bioinformatics.ic.ac.uk/geb/
A Java application developed to visualise distribution of genomic features in high resolution.
Proper citation: GEB (RRID:SCR_007395) Copy
Curated protein-protein and genetic interaction repository of raw protein and genetic interactions from major model organism species, with data compiled through comprehensive curation efforts.
Proper citation: Biological General Repository for Interaction Datasets (BioGRID) (RRID:SCR_007393) Copy
http://sourceforge.net/projects/taipan/
A fast hybrid short-read assembly tool.
Proper citation: Taipan (RRID:SCR_007330) Copy
http://bmserver.sce.ntu.edu.sg/INVERTER/
Software for a de novo exact match tandem repeat finder which main advantage is without the need to specify either the pattern or a particular pattern size, integrated with a data visualization tool and has a built-in user-friendly Graphical User Interface.
Proper citation: INVERTER (RRID:SCR_007956) Copy
http://genome.ufl.edu/rivalab/pasta/
A complete pipeline for the analysis of alternative splicing using RNA-Sequencing data.
Proper citation: PASTA (RRID:SCR_008770) Copy
http://www.raetschlab.org/suppl/qpalma
An alignment tool targeted to align spliced reads produced by Next Generation sequencing platforms such as Illumina Solexa or 454.
Proper citation: QPALMA (RRID:SCR_008791) Copy
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
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