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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
https://code.google.com/p/reditools/
A suite of python scripts to perform high-throughput investigation of RNA editing using next-generation sequencing data.
Proper citation: REDItools (RRID:SCR_012133) Copy
http://pprospector.sourceforge.net/
A pipeline of software programs to design and analyze PCR primers. It is built in Python using the open-source PyCogent toolkit.
Proper citation: PrimerProspector (RRID:SCR_012136) Copy
https://code.google.com/p/icelogo/
Software that builds on probability theory to visualize significant conserved sequence patterns in multiple peptide sequence alignments against background (reference) sequence sets that can be tailored to the studied system and the used protocol.
Proper citation: iceLogo (RRID:SCR_012137) Copy
http://musite.sourceforge.net/
A Java-based standalone application for predicting both general and kinase-specific protein phosphorylation sites.
Proper citation: Musite (RRID:SCR_012141) Copy
https://code.google.com/p/automotifserver/
Software that predicts the wide selection of 88 different types of the single amino acid post-translational modifications (PTM) in protein sequences. The source code and precompiled binaries of brainstorming tool are available under Apache licensing.
Proper citation: AMS (RRID:SCR_012140) Copy
http://sourceforge.net/projects/phosphosite/
A bioinformatical software tool for analyzing (quantitative) phosphoproteome datasets. The program retrieves kinase-substrate predictions from NetworKIN and contains various statistical modules for futher analysis.
Proper citation: PhosphoSiteAnalyzer (RRID:SCR_012142) Copy
https://code.google.com/p/hlaforest/
Software that predicts HLA haplotype by hierarchically weighting reads and using an iterative, greedy, top down pruning technique. HLAforest uses BioPerl to read in FASTA files. Alignments use Bow tie, although any alignment tool can be used to generate SAM alignments for use as input to HLAforest.
Proper citation: HLAforest (RRID:SCR_012146) Copy
http://www.bioconductor.org/packages/2.12/bioc/html/DNAcopy.html
Software that segments DNA copy number data using circular binary segmentation to detect regions with abnormal copy number.
Proper citation: DNAcopy (RRID:SCR_012560) 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://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://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
https://github.com/lpantano/seqbuster
Software tool for processing and analysis of small RNAs datasets.Reveals ubiquitous miRNA modifications in human embryonic cells.
Proper citation: SeqBuster (RRID:SCR_009616) 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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