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https://www.sourcebioscience.com/products/life-sciences-research/clones/rnai-resources/c-elegans-rnai-collection-ahringer/

C. elegans RNAi feeding library distributed by Source BioScience Ltd. Designed for genome wide study of gene function in C. elegans through loss of function studies.

Proper citation: C. elegans RNAi Collection (Ahringer) (RRID:SCR_017064) Copy   

•   Source: SciCrunch Registry

https://vertebrate.genenames.org/

Software resource for vertebrate gene nomenclature. Database of gene symbols. Coordinates with vertebrate nomenclature committees, MGNC (mouse), RGNC (rat), CGNC (chicken), AGNC (Anole green lizard), XNC (Xenopus frog) and ZNC (zebrafish), to ensure genes are named in line with their human homologs.

Proper citation: VGNC (RRID:SCR_017514) Copy   

•   Source: SciCrunch Registry

http://mirwalk.umm.uni-heidelberg.de/

Software tool to store the predicted and the experimentally validated microRNA (miRNA)-target interaction pairs. Predictions within the complete sequence of genes of human, mouse, and rat genomes. Integrates a comparative platform of miRNA-binding sites resulting from ten different prediction datasets.

Proper citation: miRWalk (RRID:SCR_016509) Copy   

•   Source: SciCrunch Registry

http://www.humphreyslab.com/SingleCell/

Software tool as analyzer for kidney single cell datasets. Allows users to query gene expression from mouse or human kidney and human kidney organoid single cell datasets. For details about datasets visit ReBuilding a Kidney website.

Proper citation: Kidney Interactive Transcriptomics (RRID:SCR_017209) Copy   

•   Source: SciCrunch Registry

https://www.alzforum.org/alzpedia

Collection of brief summaries of various genes and proteins implicated in pathophysiology of Alzheimer’s disease and other neurodegenerative disorders. It will be expanded over time and updated periodically in order to reflect current state of knowledge.

Proper citation: ALZPEDIA (RRID:SCR_017548) Copy   

•   Source: SciCrunch Registry

http://structuralbiology.cau.edu.cn/PlantGSEA/

Websever for gene set enrichment analysis of plants. Used for interpreting biological meaning of a list of genes by computing the overlaps with various previously defined gene sets.

Proper citation: PlantGSEA (RRID:SCR_016866) Copy   

•   Source: SciCrunch Registry

http://omicslab.genetics.ac.cn/dred/index.php

Database of genes related to Repeat Expansion Diseases, as comprehensive manually curated database that covers all reported repeat expansion diseases included in PubMed and OMIM. Detailed information about each repeat and its related genes/diseases can be found in database, links to OMIM, NCBI and Ensembl are also provided. Provides list of predicted genes containing unstable tandem repeats that may cause diseases via abnormal repeat expansion by support vector machine and random forest.

Proper citation: Database of genes related to Repeat Expansion Diseases (RRID:SCR_018086) Copy   

•   Source: SciCrunch Registry

https://github.com/gaow/genetic-analysis-software/blob/master/pages/GENOOM.md

Software application that implements a virtual computer world where biological entities are digital objects. In this world, each individual of a population is represented by a set of chromosomes with genetic elements (markers, genes, Quantitative Traits Loci, etc.) and attributes (phenotype, age, fertility, living status, exposure, etc.). It comes with a built-in model allowing basic genetic studies by simulations, performed according to parameter values such a penetrance matrix (phenotype probabilities for each genotype), exposure, between-relative mating probabilities, and a probability of migration in a two-dimensional migration process. The simulated populations could be analysed with different packages for statistical or genetical analysis (e.g., SAS, S-PLUS, Linkage, Mapmaker/sibs, Genehunter). Pedigrees can also be simulated according to a pedigree file at the LINKAGE format. (entry from Genetic Analysis Software)

Proper citation: GENOOM (RRID:SCR_009200) Copy   

•   Source: SciCrunch Registry

http://www.genetics.ucla.edu/software/

Software application for genetic analysis of human pedigree data under models involving a small number of loci. MENDEL is useful for segregation analysis, linkage calculations, genetic counseling, allele frequency estimation, and related kinds of problems. (entry from Genetic Analysis Software)

Proper citation: MENDEL (RRID:SCR_009288) Copy   

•   Source: SciCrunch Registry

http://watson.hgen.pitt.edu/register/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application that uses as input a trio of files: 1) a LINKAGE-format locus file modified to contain locus name information; 2) a LINKAGE-format pedigree file; and 3) a map file. Mega2 then takes this trio of input files and, via a menu-driven interface, transforms them into various other file formats, thus greatly facilitating a variety of different analyses. In addition, for many of these options, it also sets up a C-shell script that then can automatically run these analyses (if you are using Mega2 in a Unix environment that supports C-shell scripts). (entry from Genetic Analysis Software)

Proper citation: MEGA2 (RRID:SCR_009286) Copy   

•   Source: SciCrunch Registry

http://www.mapqtl.nl

Software application for mapping of quantitative trait loci (QTLs) for several types of mapping populations: BC1, F2, RILs, (doubled) haploids, full-sib family of outbreeders. Analyses: interval mapping, composite interval mapping, nonparametric mapping, automatic cofactor selection, permutation test for interval mapping. QTL charts. Everything available in an intuitive MS-Windows user interface. (entry from Genetic Analysis Software)

Proper citation: MAPQTL (RRID:SCR_009284) Copy   

•   Source: SciCrunch Registry

http://www.broad.mit.edu/ftp/distribution/software/mapmaker3/

Software application (entry from Genetic Analysis Software)

Proper citation: MAPMAKER/EXP (RRID:SCR_009281) Copy   

•   Source: SciCrunch Registry

https://github.com/gaow/genetic-analysis-software/blob/master/pages/MAPMAKER%26HOMOZ.md

Software application that calculates multipoint lod scores in pedigrees with inbreeding loops (entry from Genetic Analysis Software)

Proper citation: MAPMAKER/HOMOZ (RRID:SCR_009282) Copy   

•   Source: SciCrunch Registry

http://cougar.fhcrc.org/hplus/

An analysis tool for performing haplotype estimation on genetic markers such as SNPs and microsatellites. It is able to handle datasets that include case-control status as well as covariates and marker location variables (such as gene name, chromosome location, etc). (entry from Genetic Analysis Software)

Proper citation: HPLUS (RRID:SCR_009239) Copy   

•   Source: SciCrunch Registry

http://www.cs.helsinki.fi/u/prastas/hit/

Software application (entry from Genetic Analysis Software)

Proper citation: HIT (RRID:SCR_009236) Copy   

•   Source: SciCrunch Registry

https://github.com/gaow/genetic-analysis-software/blob/master/pages/GENETSIM.md

Software application that provides flexible simulations of family data within an easy-to-use, high-level programming language. GENETSIM has no limit on pedigree sizes or structures, or number of families, or number of marker, or number of chromosomes. Genetic transmission is modeled by first generating the locations of recombination events, and then performing gene dropping according to the given recombination pattern. Any pattern of missing data can be specified and genotyping errors can be simulated. GENETSIM can simulat multiple QTLs with pleiotropic effects, multivariate polygenic background and any number of environmental factors, age effects, epistasis and variable expression. Users can also select families based on ascertainment schemes by repeating simulations. (entry from Genetic Analysis Software)

Proper citation: GENETSIM (RRID:SCR_009199) Copy   

•   Source: SciCrunch Registry

http://vorlon.case.edu/~jxl175/HapMiner.html

Software application for association mapping based on directly mining the haplotypes from case-control data via a density-based clustering algorithm. HapMiner can be applied to whole-genome screens, as well as candidate-gene studies in small genomic regions. (entry from Genetic Analysis Software)

Proper citation: HAPMINER (RRID:SCR_009233) Copy   

•   Source: SciCrunch Registry

http://www.bioinf.mdc-berlin.de/projects/hap/

Haplotype estimation service available in two variants: one for genetic data from unrelated probands (e.g., case/control studies) and one for core family data (entry from Genetic Analysis Software)

Proper citation: HAPLOTYPE ESTIMATION (RRID:SCR_009231) Copy   

•   Source: SciCrunch Registry

http://galton.uchicago.edu/genehunterplus

Software application that is a modification of the GENEHUNTER software package which produces output files containing the null and conditional distributions of the test statistic (in nullprobs.dat and probs.dat, respectively). These files can then be used as input to the ASM program which incorporates the allele sharing modeling for lodscores and likelihood ratio tests as developed by Kong and Cox (1997). (entry from Genetic Analysis Software)

Proper citation: GENEHUNTER-PLUS (RRID:SCR_009193) Copy   

•   Source: SciCrunch Registry

http://www.biostat.jhsph.edu/~wmchen/gf.html

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 21, 2016. Software application that uses GEE method to estimate the location of the susceptibility gene based on the allele-sharing of affected sib pairs for multiple markers. GENEFINDER can further the analysis of GENEHUNTER by providing a more accurate gene location estimation and the corresponding confidence interval.

Proper citation: GENEFINDER (RRID:SCR_009190) Copy   

•   Source: SciCrunch Registry