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http://diabetes.wisc.edu/index.php

Interactive database of gene expression and diabetes related clinical phenotypes. Allows to search gene expression in tissues as a function of obesity, strain, and age, in a mouse.

Proper citation: Attie Lab Diabetes Database (RRID:SCR_016639) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/phenofam/

A web-based application that performs gene set enrichment analysis (GSEA) by employing structural and functional information on families of protein domains as annotation terms.

Proper citation: PhenoFam (RRID:SCR_000640) Copy   

•   Source: SciCrunch Registry

http://iomics.us/

A genomics data analysis platform which generates decision models for healthcare organizations and medical research. This service is meant to utilize data through machine learning methods.

Proper citation: iOMICS (RRID:SCR_000239) Copy   

•   Source: SciCrunch Registry

https://github.com/wtsi-npg/Illuminus

A fast and accurate algorithm for assigning single nucleotide polymorphism (SNP) genotypes to microarray data from the Illumina BeadArray technology.

Proper citation: ILLUMINUS (RRID:SCR_000388) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/magnolya/

A software which enables copy number variation (CNV) detections without using a reference genome. Magnolya directly compares the two next-generation sequences datasets.

Proper citation: Magnolya (RRID:SCR_000164) Copy   

•   Source: SciCrunch Registry

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

A software package that provides functions to read raw RT-qPCR data of different platforms.

Proper citation: ReadqPCR (RRID:SCR_000030) Copy   

•   Source: SciCrunch Registry

http://mzmatch.sourceforge.net/

A software to provide small tools for common processing tasks for LC/MS data. It is an extension to the metabolomics analysis pipeline mzMatch.R. The software is modular, open source, platform independent and written in Java.

Proper citation: mzMatch (RRID:SCR_000543) Copy   

•   Source: SciCrunch Registry

http://decipher.cee.wisc.edu/index.html

A software toolset that can be used for deciphering and managing DNA sequences efficiently using the R statistical programming language., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Database Enabled Code for Ideal Probe Hybridization Employing R (RRID:SCR_000581) Copy   

•   Source: SciCrunch Registry

http://www.dnastar.com/t-sub-solutions-molecular-biology-Sanger-Sequence-Assembly.aspx

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software suite for the assembly and analysis of Sanger sequencing data within the SeqMan Pro application. The software's functions include: assembling reads into groups based on sequence names, trimming vector and poor quality data, restoration of sequence ends and designing of sequence primers.

Proper citation: DNASTAR: Lasergene Core Suite (RRID:SCR_000291) Copy   

•   Source: SciCrunch Registry

https://sites.google.com/site/fdudbridge/software/pelican

Software utility for graphically editing the pedigree data files used by programs such as FASTLINK, VITESSE, GENEHUNTER and MERLIN. It can read in and write out pedigree files, saving changes that have been made to the structure of the pedigree. Changes are made to the pedigree via a graphical display interface. The resulting display can be saved as a pedigree file and as a graphical image file.

Proper citation: PELICAN (RRID:SCR_001695) Copy   

•   Source: SciCrunch Registry

http://csg.sph.umich.edu//abecasis/Metal/

Software application designed to facilitate meta-analysis of large datasets (such as several whole genome scans) in a convenient, rapid and memory efficient manner. (entry from Genetic Analysis Software)

Proper citation: METAL (RRID:SCR_002013) Copy   

•   Source: SciCrunch Registry

http://www.omicsexpress.com/sva.php

Software package to annotate, visualize, and analyze the genetic variants identified through next-generation sequencing studies, including whole-genome sequencing (WGS) and exome sequencing studies. SVA aims to provide the research community with a user-friendly and efficient tool to analyze large amount of genetic variants, and to facilitate the identification of the genetic causes of human diseases and related traits.

Proper citation: SVA (RRID:SCR_002155) Copy   

•   Source: SciCrunch Registry

https://github.com/srobb1/RelocaTE

Software toolkit of a collection of scripts in which short reads (paired or unpaired), a fasta containing the sequences of transposable elements and a reference genome sequence, are the input and the output is a series of files containing the locations of TE insertions in the reference and short reads.

Proper citation: RelocaTE (RRID:SCR_002308) Copy   

•   Source: SciCrunch Registry

https://jordan.biosci.gatech.edu/software/broadpeak/index.html

Algorithm for identifying broad peaks in diffuse ChIP-seq datasets.

Proper citation: BroadPeak (RRID:SCR_001857) Copy   

•   Source: SciCrunch Registry

http://www.vmtk.org/

Software collection of libraries and tools for 3D reconstruction, geometric analysis, mesh generation and surface data analysis for image-based modeling of blood vessels.

Proper citation: Vascular Modeling Toolkit (RRID:SCR_001893) Copy   

•   Source: SciCrunch Registry

http://wiki.c2b2.columbia.edu/califanolab/index.php/Software/ARACNE

An algorithm, using microarray expression profiles, to scale up to the complexity of regulatory networks in mammalian cells, yet general enough to address a wider range of network deconvolution problems. This method uses an information theoretic approach to eliminate the vast majority of indirect interactions typically inferred by pairwise analysis.

Proper citation: ARACNE (RRID:SCR_002180) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/science/tools/carol

Software application that is a combined functional annotation score of non-synonymous coding variants. A major challenge in interpreting whole-exome data is predicting which of the discovered variants are deleterious or neutral. To address this question in silico, they have developed a score called Combined Annotation scoRing toOL (CAROL), which combines information from two bioinformatics tools: PolyPhen-2 and SIFT, in order to improve the prediction of the effect of non-synonymous coding variants. The combination of annotation tools can help improve automated prediction of whole-genome/exome non-synonymous variant functional consequences. (entry from Genetic Analysis Software) The software should run on any UNIX or GNU/Linux system.

Proper citation: CAROL (RRID:SCR_001800) Copy   

•   Source: SciCrunch Registry

http://support.illumina.com/sequencing/sequencing_software/casava.html

Software package that creates genomic builds, calls SNPs, detects indels, and counts reads from data generated from one or more sequencing runs. In addition, CASAVA automatically generates a range of statistics, such as mean depth and percentage chromosome coverage, to enable comparison with previous builds or other samples. CASAVA analyzes sequencing reads in three stages: * FASTQ file generation and demultiplexing * Alignment to a reference genome * Variant detection and counting

Proper citation: CASAVA (RRID:SCR_001802) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/mpg/birdsuite/birdseed.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022.SNP genotyping algorithm that runs on the Affymetrix 500K, SNP5.0, and SNP6.0 platforms. This software runs a clustering algorithm and generally should be run on a sample at least 50 times. It utilizes an Expectation-Maximization (EM) algorithm to produce genotypes and confidence scores for every individual at every SNP.

Proper citation: Birdseed (RRID:SCR_001122) Copy   

•   Source: SciCrunch Registry

http://genome.sph.umich.edu/wiki/Polymutt

Software program that implemented a likelihood-based framework for calling single nucleotide variants and detecting de novo point mutation events in families for next-generation sequencing data. The program takes as input genotype likelihood format (GLF) files which can be generated following the Creation of GLF files instruction and outputs the result in the (VCF) format. The variant calling and de novo mutation detection are modelled jointly within families and can handle both nuclear and extended pedigrees without consanguinity loops. The input is a set of GLF files for each of family members and the relationships are specified through the .ped file. (entry from Genetic Analysis Software)

Proper citation: POLYMUTT (RRID:SCR_002051) Copy   

•   Source: SciCrunch Registry