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http://kissplice.prabi.fr/

Software tool that enables analysis of RNA-seq data with or without reference genome. Local transcriptome assembler for SNPs, indels and AS events.

Proper citation: KisSplice (RRID:SCR_011893) Copy   

•   Source: SciCrunch Registry

http://i122server.vu-wien.ac.at/CANGS1.1/

A user-friendly utility for processing and analyzing 454 GS-FLX data in biodiversity studies.

Proper citation: CANGS (RRID:SCR_011837) Copy   

•   Source: SciCrunch Registry

https://github.com/najoshi/sabre

Software tool to demultiplex barcoded reads into separate files. Works on both single-end and paired-end data in fastq format. Used in next generation sequencing to analyze a broad range of data.

Proper citation: sabre (RRID:SCR_011843) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/ngsep/

Software whose main functionality is the variants detector, which allows to make simultaneous discovery of SNVs, small indels, and CNVs.Accurate variant calling across species and sequencing protocols.Used for analysis of DNA high throughput sequencing data.

Proper citation: NGSEP (RRID:SCR_012827) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/affy.html

Software R package of functions and classes for the analysis of oligonucleotide arrays manufactured by Affymetrix. Used to process probe level data and for exploratory oligonucleotide array analysis.

Proper citation: affy (RRID:SCR_012835) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/edgeR/

Bioconductor software package for Empirical analysis of Digital Gene Expression data in R. Used for differential expression analysis of RNA-seq and digital gene expression data with biological replication.

Proper citation: edgeR (RRID:SCR_012802) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.psb.ugent.be/ENIGMA/

A software tool to extract gene expression modules from perturbational microarray data, based on the use of combinatorial statistics and graph-based clustering. The modules are further characterized by incorporating other data types, e.g. GO annotation, protein interactions and transcription factor binding information, and by suggesting regulators that might have an effect on the expression of (some of) the genes in the module. Version : ENIGMA 1.1 used GO annotation version : Aug 29th 2007

Proper citation: ENIGMA (RRID:SCR_013400) Copy   

•   Source: SciCrunch Registry

https://www.biodiscovery.com/search/node?keys=Imagene

Software tool as convolutional neural network to quantify natural selection from genomic data.Supervised machine learning algorithm to predict natural selection and estimate selection coefficients from population genomic data. Can be used to estimate any parameter of interest from evolutionary population genetics model., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: ImaGene (RRID:SCR_002178) Copy   

•   Source: SciCrunch Registry

http://harvester.fzk.de/harvester/

Harvester is a Web-based tool that bulk-collects bioinformatic data on human proteins from various databases and prediction servers. It is a meta search engine for gene and protein information. It searches 16 major databases and prediction servers and combines the results on pregenerated HTML pages. In this way Harvester can provide comprehensive gene-protein information from different servers in a convenient and fast manner. As full text meta search engine, similar to Google trade mark, Harvester allows screening of the whole genome proteome for current protein functions and predictions in a few seconds. With Harvester it is now possible to compare and check the quality of different database entries and prediction algorithms on a single page. Sponsors: This work has been supported by the BMBF with grants 01GR0101 and 01KW0013.

Proper citation: Bioinformatic Harvester IV (beta) at Karlsruhe Institute of Technology (RRID:SCR_008017) Copy   

•   Source: SciCrunch Registry

http://people.virginia.edu/~wc9c/TDTPC/Download.htm

Software program to compute the statistical power of the Transmission/Disequilibrium Test (TDT) analytically, based on the most accurate asymptotic algorithms up to date, and is applicable in very general situations, where different parental disease status, multiple children, mixed family type and recombination events are considered. Routine algorithms for Monte Carlo simulations with significant improvements are also implemented in this program. (entry from Genetic Analysis Software)

Proper citation: TDT-PC (RRID:SCR_001116) Copy   

•   Source: SciCrunch Registry

http://animalgene.umn.edu/locusmap/index.html

Software package designed for rapid linkage analysis and map construction of loci with a variety of inheritance modes. (entry from Genetic Analysis Software)

Proper citation: LOCUSMAP (RRID:SCR_000840) Copy   

•   Source: SciCrunch Registry

http://www.rightfield.org.uk/

An open-source tool for adding ontology term selection to Excel spreadsheets. It is used by a "Template Creator" to create semantically aware Excel spreadsheet templates. The Excel templates are then reused by Scientists to collect and annotate their data; without any need to understand, or even be aware of, RightField or the ontologies used. For each annotation field, RightField can specify a range of allowed terms from a chosen ontology (subclasses, individuals or combinations). The resulting spreadsheet presents these terms to the users as a simple drop-down list. This reduces the adoption barrier for using community ontologies as the annotation is made by the scientist that generated the data rather than a third party, and the annotation is collected at the time of data collection. RightField is a standalone Java application which uses Apache-POI for interacting with Microsoft documents. It enables users to import Excel spreadsheets, or generate new ones from scratch. Ontologies can either be imported from their local file systems, or from the BioPortal ontology repository. Individual cells, or whole columns or rows can be marked with the required ranges of ontology terms and an individual spreadsheet can be annotated with terms from multiple ontologies.

Proper citation: RightField (RRID:SCR_002649) Copy   

•   Source: SciCrunch Registry

http://www.altanalyze.org/

Software application for microarry, RNA-Seq and metabolomics analysis. For splicing sensitive platforms (RNA-Seq or Affymetrix Exon, Gene and Junction arrays), it will assess alternative exon (known and novel) expression along protein isoforms, domain composition and microRNA targeting. In addition to splicing-sensitive platforms, it provides comprehensive methods for the analysis of other data (RMA summarization, batch-effect removal, QC, statistics, annotation, clustering, network creation, lineage characterization, alternative exon visualization, gene-set enrichement and more). AltAnalyze can be run through an intuitive graphical user interface or command-line and requires no advanced knowledge of bioinformatics programs or scripting. Alternative regulated exons can be subsequently visualized in the context of proteins, domains and microRNA binding sites with the Cytoscape Plugin DomainGraph.

Proper citation: AltAnalyze - Alternative Splicing Analysis Tool (RRID:SCR_002951) Copy   

•   Source: SciCrunch Registry

https://sites.google.com/a/brain.org.au/ctp/

Software package with functions that will help researchers plan how many subjects per group need to be included in an MRI-based cortical thickness study to ensure a thickness difference is detected. The package requires cortical thickness mapping and co-registration to be carried out using Freesurfer. The power analyses are implemented in the R software package., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: cortex (RRID:SCR_002467) Copy   

•   Source: SciCrunch Registry

https://ccg.murdoch.edu.au/yabi/login/?next=/yabi/

A web-based analytical environment framework for bioinformatics applications that can be customized for a diverse range of -omics applications. The software system is adaptable to a range of both pluggable execution and data backends in an open source implementation. Enabling seamless and transparent access to heterogenous HPC environments at its core, it then provides an analysis workflow environment that can create and reuse workflows as well as manage large amounts of both raw and processed data in a secure and flexible way across geographically distributed compute resources. Yabi can be used via a web-based environment to drag-and-drop tools to create sophisticated workflows. It can also be accessed through the Yabi command line which is designed for users that are more comfortable with writing scripts or for enabling external workflow environments to leverage the features in Yabi. Configuring tools can be a significant overhead in workflow environments. Yabi greatly simplifies this task by enabling system administrators to configure as well as manage running tools via a web-based environment and without the need to write or edit software programs or scripts.

Proper citation: Yabi (RRID:SCR_005359) Copy   

•   Source: SciCrunch Registry

http://bioinf.wehi.edu.au/folders/melanie/haploclusters.html

Software program designed to detect excess haplotypes sharing in datasets consisting of case and control haplotypes. Excess haplotype sharing can be seen around disease loci in case samples since LD persists longer here than in the controls where LD is persisting only according to the relatedness of the individuals in the population, i.e. the age of the population. (entry from Genetic Analysis Software)

Proper citation: HAPLOCLUSTERS (RRID:SCR_007439) Copy   

•   Source: SciCrunch Registry

https://www.jurgott.org/linkage/LinkagePC.html

Standard software package for genetic linkage called LINKAGE. Genetic linkage analysis is statistical technique used to map genes and find approximate location of disease genes.

Proper citation: LINKAGE (RRID:SCR_007033) Copy   

•   Source: SciCrunch Registry

http://compgen.rutgers.edu/multimap.shtml

Software program for automated construction of genetic maps (entry from Genetic Analysis Software)

Proper citation: MULTIMAP (RRID:SCR_007168) Copy   

•   Source: SciCrunch Registry

http://csg.sph.umich.edu/boehnke/sibmed.php

Software application that identifies likely genotyping errors and mutations for a sib pair in the context of multipoint mapping. (entry from Genetic Analysis Software)

Proper citation: SIBMED (RRID:SCR_007495) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.ua.pt/coeus/

A semantic web-powered knowledge management framework, aiming at a streamlined application development cycle and following a semantic web in a box approach. The framework provides a single package including advanced data integration and triplification tools, base ontologies, a web-oriented engine and a flexible exploration API. Resources can be integrated from heterogeneous sources, including CSV and XML files or SQL and SPARQL query results, and mapped directly to one or more ontologies. Advanced interoperability features include REST services, a SPARQL endpoint and LinkedData publication. These enable the creation of multiple applications for web, desktop or mobile environments, and empower a new knowledge federation layer. It is targeted at rapid application deployment of new applications in any research field, supported by a comprehensive integration engine and an advanced data distribution API.

Proper citation: COEUS (RRID:SCR_006287) Copy   

•   Source: SciCrunch Registry