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http://vortex.cs.wayne.edu/projects.htm#Onto-Design

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Many Laboratories chose to design and print their own microarrays. At present, the choice of the genes to include on a certain microarray is a very laborious process requiring a high level of expertise. Onto-Design database is able to assist the designers of custom microarrays by providing the means to select genes based on their experiment. Design custom microarrays based on GO terms of interest. User account required. Platform: Online tool

Proper citation: Onto-Design (RRID:SCR_000601) Copy   

•   Source: SciCrunch Registry

http://www-rcf.usc.edu/~gqian/software.htm (not available)

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software application (entry from Genetic Analysis Software)

Proper citation: MRH (RRID:SCR_000841) Copy   

•   Source: SciCrunch Registry

http://www.biosciences-labs.bham.ac.uk/Kearsey/

Software application providing a user freiendly way to perform QTL analysis. The software currently allows 3 types of QTL analysis: (1) single marker ANOVA. (2) marker regression. (3) interval mapping by regression. (entry from Genetic Analysis Software)

Proper citation: QTL CAFE (RRID:SCR_000844) 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://wwwchg.duhs.duke.edu/research/osa.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. Software application that allows the researcher to evaluate evidence for linkage even when heterogeneity is present in a data set. This is not an unusual occurrence when studying diseases of complex origin. Families are ranked by covariate values in order to test evidence for linkage among homogeneous subsets of families. Because families are ranked, a priori covariate cutpoints are not necessary. Covariates may include linkage evidence at other genes, environmental exposures, or biological trait values such as cholesterol, age at onset, and so on.

Proper citation: OSA (RRID:SCR_002016) 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

https://biobank.partners.org/for-researchers

Blood biobank for the Partners research program, which investigates the affects of genes, lifestyle and environment on human health.

Proper citation: Partners HealthCare Biobank (RRID:SCR_001316) 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

http://david.abcc.ncifcrf.gov/content.jsp?file=/ease/ease1.htm&type=1

Windows(c) desktop software application, customizable and standalone, that facilitates the biological interpretation of gene lists derived from the results of microarray, proteomic, and SAGE experiments. Provides statistical methods for discovering enriched biological themes within gene lists, generates gene annotation tables, and enables automated linking to online analysis tools. Offers statistical models to deal with multi-test comparison problem. Platform: Windows compatible

Proper citation: EASE: the Expression Analysis Systematic Explorer (RRID:SCR_013361) Copy   

•   Source: SciCrunch Registry

https://github.com/aertslab/SCENIC

Software R package as single cell regulatory network inference and clustering. Used for simultaneous gene regulatory network reconstruction and cell state identification from single cell RNA-seq data.

Proper citation: SCENIC (RRID:SCR_017247) Copy   

•   Source: SciCrunch Registry

https://www.thermofisher.com/order/catalog/product/4363993

Software tool by Applied Biosystems to design primers and probes using TaqMan and SYBR Green I dye chemistries for gene quantitation and allelic discrimination (SNP) real-time PCR applications. Developed for use with StepOne, StepOnePlus, 7300, 7500, 7500 Fast, 7900HT, ViiA 7, and QuantStudio real-time PCR systems. Provides customized application specific documents for absolute⁄relative quantitation and allelic discrimination.

Proper citation: Primer Express Software (RRID:SCR_017376) Copy   

•   Source: SciCrunch Registry

https://www.4dnucleome.org

Research project to understand the principles underlying nuclear organization in space and time, the role nuclear organization plays in gene expression and cellular function, and how changes in nuclear organization affect normal development and diseases. Portal provides free access to datasets, software packages, and protocols to advance biomedical research of nuclear architecture. Aims to develop and apply approaches to map the structure and dynamics of the human and mouse genomes.

Proper citation: 4D Nucleome (RRID:SCR_016925) Copy   

•   Source: SciCrunch Registry

https://hub.docker.com/r/mziemann/tallyup/

Docker image that is used to process all of the data present in the Digital Expression Explorer 2 dataset. It can be freely used by anyone to process data on NCBI SRA or process their own RNA-seq fastq files. Used for bulk reprocessing of public RNA-seq data from SRA. The pipeline tallies the reads assigned to each gene or transcript.

Proper citation: Digital Expression Explorer 2 Docker Image (RRID:SCR_016931) Copy   

•   Source: SciCrunch Registry

http://ophid.utoronto.ca/mirDIP/

microRNA data integration portal to find microRNAs that target a gene, or genes targeted by a microRNA, in Homo sapiens. Software to integrate prediction databases to elucidate accurate microRNA:target relationships. Used for human microRNA prediction studies.

Proper citation: mirDIP (RRID:SCR_016770) Copy   

•   Source: SciCrunch Registry

http://cab.spbu.ru/software/rnaquast/

Software tool for evaluating RNA-Seq assembly quality and benchmarking transcriptome assemblers using reference genome and gene database. Capable to estimate gene database coverage by raw reads and de novo quality assessment using third party software.

Proper citation: rnaQUAST (RRID:SCR_016994) Copy   

•   Source: SciCrunch Registry

http://galaxy.cineca.it/fusion/main

Portal provides an easy access to a comprehensive database designed for storing, displaying and annotating gene fusion events detected from NGS data. It can query a database of somatic fusion genes events predicted and annotated starting from paired-end RNA-seq data.

Proper citation: LiGeA (RRID:SCR_015940) Copy   

•   Source: SciCrunch Registry

https://github.com/lufuhao/AutoEVM

Software tool as Autorun Evidence Modeler. Requires EVidenceModeler (aka EVM) software which combines ab into gene predictions and protein and transcript alignments into weighted consensus gene structures.

Proper citation: AutoEVM (RRID:SCR_017556) Copy   

•   Source: SciCrunch Registry

http://faculty.washington.edu/browning/presto/presto.html

Software application that performs permutation testing and computes empirical distributions of order statistics for one and two stage association studies with stratified or unstratified data.

Proper citation: PRESTO: Genetic Association Analysis Software (RRID:SCR_013285) Copy   

•   Source: SciCrunch Registry

http://genecanvas.ecgene.net/#!index.md#THESIAS:_testing_haplotype_effects_in_association_studies

Software program that performs haplotype-based association analysis in unrelated individuals. This program is based on a maximum likelihood model described in Tregouet et al. 2002 and is linked to the stochastic EM (SEM) algorithm. THESIAS allows the simultaneous estimation of haplotype frequencies and of their associated effects on the phenotype of interest. In its current version, both quantitative and qualitative phenotypes can be studied. Covariate-adjusted haplotype effects as well as haplotype x covariate interactions can be investigated. (entry from Genetic Analysis Software)

Proper citation: THESIAS (RRID:SCR_013449) Copy   

•   Source: SciCrunch Registry

http://www.dmle.org/

Software application for high-resolution mapping of the position of a disease mutation relative to a set of genetic markers using population linkage disequilibrium (LD). (entry from Genetic Analysis Software)

Proper citation: DMLE (RRID:SCR_013454) Copy   

•   Source: SciCrunch Registry