Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
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.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
TOMCAT Resource Report Resource Website 10+ mentions |
TOMCAT (RRID:SCR_013120) | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May24,2023. Software program that implements the Mantel statistics as proposed by Beckmann et al. (2005) to test for association between genetic markers and phenotypes in case-control studies using haplotype information. The potential value of haplotypes has attracted widespread interest in the mapping of complex traits. Haplotype sharing methods take into account linkage disequilibrium information between multiple markers, and may have good power to detect predisposing genes. We present a new approach based on Mantel statistics for space time clustering, which we developed in order to improve the power of haplotype sharing analysis for gene mapping in complex disease. The new statistic correlates genetic similarity and phenotypic similarity across pairs of haplotypes for case-only and case-control studies. The genetic similarity is measured as the shared length between haplotypes around a putative disease locus. Alternative measures for the phenotypic similarity were implemented. (entry from Genetic Analysis Software) | gene, genetic, genomic, java, 5.0 | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154681 | SCR_013120 | 2026-09-12 01:02:48 | 18 | |||||||||
|
SASQUANT Resource Report Resource Website 1+ mentions |
SASQUANT (RRID:SCR_013122) | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. SAS software program to estimate genetic effects and heritabilities of quantitative traits in breeding populations consisting of six related generations (entry from Genetic Analysis Software) | gene, genetic, genomic, sas, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154610, biotools:sasquant | https://bio.tools/sasquant | SCR_013122 | 2026-09-12 01:02:48 | 4 | ||||||||
|
SCORE-SEQ Resource Report Resource Website 1+ mentions |
SCORE-SEQ (RRID:SCR_013121) | software application, software resource | A command-line program for detecting disease associations with rare variants in sequencing studies. The mutation information is aggregated across multiple variant sites of a gene through a weighted linear combination and then related to disease phenotypes through appropriate regression models. The weights can be constant or dependent on allele frequencies and phenotypes. The association testing is based on score-type statistics. The allele-frequency threshold can be fixed or variable. Statistical significance can be assessed by using asymptotic normal approximation or resampling. The current release covers binary and continuous traits with arbitrary covariates under case-control and cross-sectional sampling. (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154611 | SCR_013121 | SCORE-type tests for detecting disease associations with rare variants in SEQuencing Studies | 2026-09-12 01:02:48 | 6 | |||||||||
|
QMSIM Resource Report Resource Website 50+ mentions |
QMSIM (RRID:SCR_013123) | software application, software resource | Software application designed to simulate a wide range of genetic architectures and population structures in livestock. Large scale genotyping data and complex pedigrees can be efficiently simulated. QMSim is a family based simulator, which can also take into account predefined evolutionary features, such as LD, mutation, bottlenecks and expansions. The simulation is basically carried out in two steps: In the first step, a historical population is simulated to establish mutation-drift equilibrium and, in the second step, recent population structures are generated, which can be complex. QMSim allows for a wide range of parameters to be incorporated in the simulation models in order to produce appropriate simulated data. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, ms-windows, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154560, biotools:qmsim | https://bio.tools/qmsim | SCR_013123 | Qtl and Marker SIMulator | 2026-09-12 01:02:48 | 63 | ||||||||
|
INSEGT Resource Report Resource Website |
INSEGT (RRID:SCR_013126) | software application, software resource | Software application that constructs feasible haplotype configurations and the corresponding segregation types on pedigrees. the haplotype configuration minimizes recombinations on the pedigree. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, (the standard template library, stl, is used) | is listed by: Genetic Analysis Software | nlx_154412 | SCR_013126 | INference of SEGregation Types PANGAEA | 2026-09-12 01:02:48 | 0 | |||||||||
|
Solar Eclipse Imaging Genetics tools Resource Report Resource Website 10+ mentions |
Solar Eclipse Imaging Genetics tools (RRID:SCR_009645) | Solar Eclipse Imaging Genetics tools | software application, software resource | Software tools optimized for performing univariate and multivariate imaging genetics analyses while providing practical correction strategies for multiple testing. The goal of this project is to merge two important research directions in modern science, genetics and neuroimaging. This entails combining modern statistical genetic methods and quantitative phenotyping performed with high dimensional neuroimaging modalities. So far, however, standard imaging tools are unable to deal with large-scale genetics data, and standard genetics tools, in turn, are unable to accommodate large size and binary format of the image data. Their focus is to create imaging genetics tools for classical genetic and epigenetic epidemiological analyses such as heritability, pleiotropy, quantitative trait loci (QTL) and genome-wide association (GWAS), gene expression, and methylation analyses optimized for traits derived from structural and functional brain imaging data | c++, genetic association, genomic analysis, gifti, imaging genomics, linux, loni pipeline, macos, microsoft, nifti, posix/unix-like, snp, gene, windows, windows xp, genetics, neuroimaging, heritability, pleiotropy, quantitative trait loci, genome-wide association, gene expression, methylation, trait, structural neuroimaging, functionalneuroimaging, brain imaging | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Non-commercial, Open Software License, v3, Http://www.nitrc.org/include/glossary.php#552 | nlx_155966 | SCR_009645 | 2026-09-12 01:02:47 | 14 | ||||||||
|
GLFSINGLE/GLFTRIO/GLFMULTIPLES Resource Report Resource Website 1+ mentions |
GLFSINGLE/GLFTRIO/GLFMULTIPLES (RRID:SCR_013128) | software application, software resource | Software application that is a GLF-based variant caller for next-generation sequencing data. It takes one/three/multiple GLF format genotype likelihood files as input and generates a VCF-format set of variant calls as output. (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154358 | SCR_013128 | 2026-09-12 01:02:48 | 1 | ||||||||||
|
GGSD Resource Report Resource Website |
GGSD (RRID:SCR_013129) | software application, software resource | Web-based, relational database driven data management software package for the management of large scale genetic studies. (entry from Genetic Analysis Software) | gene, genetic, genomic, java, php, perl, web-based | is listed by: Genetic Analysis Software | nlx_154355 | SCR_013129 | Generic Genetic Studies Database | 2026-09-12 01:02:48 | 0 | |||||||||
|
Movement Disorders Biobank Resource Report Resource Website |
Movement Disorders Biobank (RRID:SCR_010659) | MDBB | biomaterial supply resource, material resource | A biobank of human biological material and genetic information. It provides samples and information to researchers in order to identify new genes and clarify pathogenic mechanisms of diseases. The biobank offers biochemical and molecular diagnoses of genetic dystonias, Parkinson's disease and NBIA disorders, as well as storage of biological samples for external institutions. | dna, fibroblast, movement disorder, neurodegeneration, brain iron accumulation disorder, dystonia, parkinson's disease, phenotype, genotype, gene, biobank |
is listed by: One Mind Biospecimen Bank Listing is related to: EuroBioBank has parent organization: EuroBioBank |
Movement disorder, Neurodegeneration with Brain Iron Accumulation disorder, Dystonia, Parkinson's disease | nlx_69108 | http://www.istituto-besta.it/Area-Ricerca.aspx?doc=Elenco-Unita-Operative&IdUO=UO-NEUROGENETICAMOLECOLARE | SCR_010659 | 2026-09-12 01:02:47 | 0 | |||||||
|
Berkeley Drosophila Genome Project Resource Report Resource Website 100+ mentions |
Berkeley Drosophila Genome Project (RRID:SCR_013094) | BDGP, BDGP EST, BDGP INS | data or information resource, database | Database on the sequence of the euchromatic genome of Drosophila melanogaster In addition to genomic sequencing, the BDGP is 1) producing gene disruptions using P element-mediated mutagenesis on a scale unprecedented in metazoans; 2) characterizing the sequence and expression of cDNAs; and 3) developing informatics tools that support the experimental process, identify features of DNA sequence, and allow us to present up-to-date information about the annotated sequence to the research community. Resources * Universal Proteomics Resource: Search for clones for expression and tissue culture * Materials: Request genomic or cDNA clones, library filters or fly stocks * Download Sequence data sets and annotations in fasta or xml format by http or ftp * Publications: Browse or download BDGP papers * Methods: BDGP laboratory protocols and vector maps * Analysis Tools: Search sequences for CRMs, promoters, splice sites, and gene predictions * Apollo: Genome annotation viewer and editor September 15, 2009 Illumina RNA-Seq data from 30 developmental time points of D. melanogaster has been submitted to the Short Read Archive at NCBI as part of the modENCODE project. The data set currently contains 2.2 billion single-end and paired reads and over 201 billion base pairs. | drosophila genome, cdna, est, transposon insertions, genomic sequencing, gene, FASEB list |
is related to: Bgee: dataBase for Gene Expression Evolution is related to: OpenFlyData.org has parent organization: University of California at Berkeley; Berkeley; USA is parent organization of: Patterns of Gene Expression in Drosophila Embryogenesis |
NHGRI ; NIGMS |
PMID:21177961 | nif-0000-02867, r3d100010624 | http://www.bdgp.org/ | SCR_013094 | 2026-09-12 01:02:48 | 478 | ||||||
|
WHAIT Resource Report Resource Website |
WHAIT (RRID:SCR_009425) | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software application (entry from Genetic Analysis Software). | gene, genetic, genomic | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154691 | SCR_009425 | Weighted Haplotype test And an Imputation-based Test. | 2026-09-12 01:02:46 | 0 | ||||||||
|
ZAPLO Resource Report Resource Website 1+ mentions |
ZAPLO (RRID:SCR_009426) | ZAPLO | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. | gene, genetic, genomic, linux, unix, solaris | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154692 | SCR_009426 | 2026-09-12 01:02:46 | 3 | ||||||||
|
UNKNOWN Resource Report Resource Website 10+ mentions |
UNKNOWN (RRID:SCR_009423) | UNKNOWN | software application, software resource | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154684 | SCR_009423 | LINKAGE - general pedigrees | 2026-09-12 01:02:46 | 14 | ||||||||
|
TFPGA Resource Report Resource Website 50+ mentions |
TFPGA (RRID:SCR_009421) | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software program that calculates descriptive statistics, genetic distances, and F-statistics. It also performs tests for Hardy-Weinberg equilibrium, exact tests for genetic differentiation, Mantel tests, and UPGMA cluster analyses. (entry from Genetic Analysis Software) | gene, genetic, genomic, ms-windows | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154680 | SCR_009421 | Tools For Population Genetic Analyses | 2026-09-12 01:02:46 | 57 | ||||||||
|
ENDOG Resource Report Resource Website 100+ mentions |
ENDOG (RRID:SCR_013289) | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1, 2023. Software application that calculates individual inbreeding (F) and average relatedness (AR) coefficients. Additionally, users can compute useful parameters in population genetics such as: the number of ancestors explaining genetic variability; the genetic importance of the herds; F statistics from genealogical information. (entry from Genetic Analysis Software) | gene, genetic, genomic, fortran 77 | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154299 | SCR_013289 | 2026-09-12 01:02:48 | 120 | |||||||||
|
WEIGHTED FDR Resource Report Resource Website |
WEIGHTED FDR (RRID:SCR_013442) | software application, software resource | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, r, ms-windows, linux, unix, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154604, SCR_000848, nlx_154690, biotools:weighted_fdr | https://bio.tools/weighted_fdr | SCR_013442 | R/WEIGHTED_FDR | 2026-09-12 01:02:49 | 0 | ||||||||
|
GenGen Resource Report Resource Website 10+ mentions |
GenGen (RRID:SCR_013447) | GenGen | software application, software resource | A suite of free software tools to facilitate the analysis of high-throughput genomics data sets. The package is currently a work-in-progress and infrequently updated. | genomic analysis, imaging genomics, pathway, network, snp, gene, genetics, genomics |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: OpenBioinformatics.org |
Free | nlx_155766 | http://www.nitrc.org/projects/gengen | SCR_013447 | GenGen: Genetic Genomics Analysis of Complex Data | 2026-09-12 01:02:49 | 26 | ||||||
|
MENDELSOFT Resource Report Resource Website |
MENDELSOFT (RRID:SCR_013177) | software application, software resource | Software application for identifying all Mendelian inconsistencies in complex pedigree data with thousand of individuals, including many loops and several errors. Can also infer missing genotypes. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, unix, linux/cygwin, ms-windows, macos | is listed by: Genetic Analysis Software | nlx_154474 | SCR_013177 | 2026-09-12 01:02:48 | 0 | ||||||||||
|
BEAGLECALL Resource Report Resource Website 1+ mentions |
BEAGLECALL (RRID:SCR_013301) | BEAGLECALL | software application, software resource | Software package for simultaneous genotype calling and haplotype phasing for unrelated individuals. BEAGLECALL produces output posterior genotype probabilities and output phased haplotypes. BEAGLECALL generates extremely accurate genotype calls because it uses both allele signal intensity data and inter-marker correlation to call genotypes. BEAGLECALL is designed for use with high-density SNP arrays, and it uses the BEAGLE haplotype frequency model to model inter-marker correlation. (entry from Genetic Analysis Software) | gene, genetic, genomic, java, ms-windows, unix, linux, macos | is listed by: Genetic Analysis Software | nlx_154239 | SCR_013301 | 2026-09-12 01:02:48 | 1 | |||||||||
|
SPREG Resource Report Resource Website 1+ mentions |
SPREG (RRID:SCR_013261) | SPREG | software application, software resource | Software program for performing regression analysis of secondary phenotype data in case-control association studies. Secondary phenotypes are quantitative or qualitative traits other than the case-control status. Because the case-control sample is not a random sample of the general population, standard statistical analysis of secondary phenotype data can yield very misleading results. SPREG implements valid and efficient statistical methods. (entry from Genetic Analysis Software) | gene, genetic, genomic, c | is listed by: Genetic Analysis Software | nlx_154660 | SCR_013261 | Secondary Phenotype REGression analysis | 2026-09-12 01:02:48 | 2 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the NIF Resources search. From here you can search through a compilation of resources used by NIF and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that NIF has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on NIF then you can log in from here to get additional features in NIF such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into NIF you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
