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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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BREAKDANCER Resource Report Resource Website 100+ mentions |
BREAKDANCER (RRID:SCR_001799) | BreakDancer | software application, software resource | A Perl/C++ software package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. BreakDancerMax predicts five types of structural variants: insertions, deletions, inversions, inter- and intra-chromosomal translocations from next-generation short paired-end sequencing reads using read pairs that are mapped with unexpected separation distances or orientation. (entry from Genetic Analysis Software) | gene, genetic, genomic, perl, c++, next generation sequencing, structural variant, insertion, deletion, inversion, inter-chromosomal translocation, intra-chromosomal translocation, chromosomal translocation, indel, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA |
PMID:19668202 | Free, Available for download, Freely available | biotools:breakdancer, nlx_154253, OMICS_00307 | https://bio.tools/breakdancer | SCR_001799 | 2026-02-15 09:18:10 | 370 | ||||||
|
HAPLOPAINTER Resource Report Resource Website 10+ mentions |
HAPLOPAINTER (RRID:SCR_001710) | HaploPainter | software application, software resource | A pedigree drawing program, suitable in processing haplotype outputs from GENEHUNTER, ALLEGRO, MERLIN, and SIMWALK (entry from Genetic Analysis Software) | gene, genetic, genomic, perl, pedigree, haplotype, draw, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:15377505 | Free, Freely Available | nlx_154062, OMICS_00209, biotools:haplopainter | https://bio.tools/haplopainter | http://haplopainter.sourceforge.net/html/ManualIndex.htm | SCR_001710 | 2026-02-15 09:18:09 | 45 | |||||
|
PEDHUNTER Resource Report Resource Website 1+ mentions |
PEDHUNTER (RRID:SCR_002031) | PedHunter | software application, software resource | Software package that facilitates creation and verification of pedigrees within large genealogies. The pedigrees are produced as files in LINKAGE format ready for linkage analysis and for drawing with a variety of drawing programs, such as PEDDRAW and cranefoot. | gene, genetic, genomic, genealogy, pedigree, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: NCBI |
PMID:20433770 PMID:9521925 |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:pedhunter, OMICS_00211, nlx_154518 | https://bio.tools/pedhunter | SCR_002031 | 2026-02-15 09:18:13 | 2 | ||||||
|
SYZYGY Resource Report Resource Website 1+ mentions |
SYZYGY (RRID:SCR_002157) | Syzygy | software application, software resource | A targeted sequencing post processing analysis software tool that allows: 1. SNP and indel detection; 2. Allele frequency estimation; 3. Single-marker association test; 4. Group-wise marker test association; 5. Experimental QC summary (%dbSNP, Ts/Tv, Ns/S); 6. Power to detect variant. (entry from Genetic Analysis Software) | gene, genetic, genomic, variant calling, snp, indel, allele frequency, single-marker association, group-wise marker, quality control, variant |
is listed by: OMICtools is listed by: Genetic Analysis Software has parent organization: Broad Institute |
PMID:21983784 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154668, OMICS_02166 | SCR_002157 | Syzygy - SNP and indel calling for pooled and individual targeted resequencing studies | 2026-02-15 09:18:15 | 5 | ||||||
|
Sequence Search and Alignment by Hashing Algorithm Resource Report Resource Website 1+ mentions |
Sequence Search and Alignment by Hashing Algorithm (RRID:SCR_000544) | SSAHA2 | source code, software resource | A program designed for the efficient mapping of sequence reads onto genomic references. The software is capable of reading most sequencing platforms and giving a range of outputs are supported. | sequence, genomic, analysis, search, alignment, algorithm, mapping, bio.tools |
is listed by: OMICtools is listed by: bio.tools is related to: SMALT has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:11591649 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:ssaha2, OMICS_00690, nlx_93831 | https://bio.tools/ssaha2 | SCR_000544 | ssaha2, ssaha, Sequence Search and Alignment by Hashing Algorithm | 2026-02-15 09:17:56 | 6 | |||||
|
MF-GE Resource Report Resource Website |
MF-GE (RRID:SCR_003509) | MF-GE | source code, software resource | A hybrid software system for feature selection and sample classification of high-dimensional datasets. It is designed for microarray but can be applied to any other high-dimensional datasets. It uses multiple filters to produce a normalized score for each feature. The score is an indication of the usefulness of each feature. It is then translated into a frequency map with more useful features receive a higher frequency in the map. | microarray, classification, gene |
is listed by: OMICtools has parent organization: University of Sydney; Sydney; Australia |
PMID:20122224 | OMICS_02295 | SCR_003509 | Multiple Filters enhanced Genetic Ensemble System (MF-GE), Multiple Filters enhanced Genetic Ensemble System | 2026-02-15 09:18:31 | 0 | |||||||
|
BamView Resource Report Resource Website 10+ mentions |
BamView (RRID:SCR_004207) | BamView | source code, software resource | A free interactive display of read alignments in BAM data files that can be launched with Java Web Start or downloaded. This interactive Java application for visualizing the large amounts of data stored for sequence reads which are aligned against a reference genome sequence can be used in a number of contexts including SNP calling and structural annotation. It has been integrated into Artemis so that the reads can be viewed in the context of the nucleotide sequence and genomic features. The source code is available as part of the Artemis code which can be downloaded from GitHub. | bam, next-generation sequencing, java, snp calling, structural annotation, macosx, unix, windows, visualize, analyze, sequence read, reference sequence, single nucleotide polymorphism, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:22253280 PMID:20071372 |
GNU General Public License | biotools:bamview, OMICS_00878, nlx_22933 | https://bio.tools/bamview | SCR_004207 | 2026-02-15 09:18:42 | 21 | ||||||
|
Genomedata Resource Report Resource Website |
Genomedata (RRID:SCR_004544) | Genomedata | source code, software resource | A format for efficient storage of multiple tracks of numeric data anchored to a genome. The format allows fast random access to hundreds of gigabytes of data, while retaining a small disk space footprint. They have also developed utilities to load data into this format. Retrieving data from this format is more than 2900 times faster than a naive approach using wiggle files. A reference implementation in Python and C components is available here under the GNU General Public License. The software has only been tested on Linux and Mac systems. | genome, data, format, linux, mac, functional genomics, function, bio.tools |
is listed by: OMICtools is listed by: 3DVC is listed by: bio.tools is listed by: Debian has parent organization: University of Washington; Seattle; USA |
PMID:20435580 | GNU General Public License | nlx_53677, biotools:genomedata, OMICS_02148 | https://bio.tools/genomedata | SCR_004544 | 2026-02-15 09:18:45 | 0 | ||||||
|
Visual Molecular Dynamics Resource Report Resource Website 100+ mentions |
Visual Molecular Dynamics (RRID:SCR_001820) | VMD | source code, software resource | A molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code. | standalone software, mac os x, unix, virtual machine, windows, c++ |
is listed by: OMICtools has parent organization: University of Illinois at Urbana-Champaign; Illinois; USA |
NIGMS | PMID:8744570 | Free, Freely available | OMICS_03804 | SCR_001820 | 2026-02-15 09:18:11 | 378 | ||||||
|
R/QTL Resource Report Resource Website 500+ mentions |
R/QTL (RRID:SCR_009085) | R/QTL | software application, software resource | Software program for mapping quantitative trait loci in experimental crosses. (entry from Genetic Analysis Software) | gene, genetic, genomic, c and r, unix, ms-windows, macos |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: OMICtools |
DOI:10.1093/bioinformatics/btg112 | OMICS_07093, nlx_154097 | https://sources.debian.org/src/r-cran-qtl/ | SCR_009085 | 2026-02-15 09:20:03 | 987 | |||||||
|
FASTLINK Resource Report Resource Website 50+ mentions |
FASTLINK (RRID:SCR_009177) | FASTLINK | software application, software resource | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, c, unix, vms, ms-dos, .. and can also run in parallel on shared memory unix machines |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: OMICtools |
PMID:8807326 | OMICS_28405, nlx_154309 | https://sources.debian.org/src/fastlink/ | SCR_009177 | faster version of LINKAGE LINKAGE | 2026-02-15 09:19:39 | 58 | ||||||
|
LAMARC Resource Report Resource Website 10+ mentions |
LAMARC (RRID:SCR_009252) | LAMARC | software application, software resource | Software application that estimates effective population sizes, exponential population growth rates, and past migration rates between two or n populations, and simultaneously estimates the per-nucleotide recombination rate. Currently Lamarc can use DNA or RNA sequence data, SNP data, and microsatellite data. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, linux, ms-windows, macos |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: OMICtools |
DOI:10.1016/j.tree.2008.09.007 | OMICS_28408, nlx_154420 | https://sources.debian.org/src/lamarc/ | SCR_009252 | Likelihood Analysis with Metropolis Algorithm using Random Coalescence | 2026-02-15 09:20:09 | 46 | ||||||
|
MINIMAC Resource Report Resource Website 100+ mentions |
MINIMAC (RRID:SCR_009292) | MINIMAC | software application, software resource | Software application that is a low memory, computationally efficient implementation of the MaCH algorithm for genotype imputation. It is designed to work on phased genotypes and can handle very large reference panels with hundreds or thousands of haplotypes. The name has two parts. The first, mini, refers to the modest amount of computational resources it requires. The second, mac, is short hand for MaCH, our widely used algorithm for genotype imputation. (entry from Genetic Analysis Software) | gene, genetic, genomic |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: OMICtools is related to: Michigan Imputation Server |
DOI:10.1038/ng.3656 | nlx_154483, OMICS_08953 | https://sources.debian.org/src/minimac4/ | SCR_009292 | MACH | 2026-02-15 09:20:00 | 187 | ||||||
|
PEER Resource Report Resource Website 500+ mentions |
PEER (RRID:SCR_009326) | PEER | software application, software resource | Software collection of Bayesian approaches to infer hidden determinants and their effects from gene expression profiles using factor analysis methods. Applications of PEER have * detected batch effects and experimental confounders * increased the number of expression QTL findings by threefold * allowed inference of intermediate cellular traits, such as transcription factor or pathway activations This project offers an efficient and versatile C++ implementation of the underlying algorithms with user-friendly interfaces to R and python. | gene, genetic, genomic, c++, r, python |
is listed by: Genetic Analysis Software is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:21283789 PMID:20463871 |
nlx_154532, OMICS_04597 | https://github.com/PMBio/peer/wiki | SCR_009326 | 2026-02-15 09:20:01 | 553 | |||||||
|
ANNOVAR Resource Report Resource Website 5000+ mentions |
ANNOVAR (RRID:SCR_012821) | ANNOVAR | software application, software resource | An efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, as well as mouse, worm, fly, yeast and many others). Given a list of variants with chromosome, start position, end position, reference nucleotide and observed nucleotides, ANNOVAR can perform: 1. gene-based annotation. 2. region-based annotation. 3. filter-based annotation. 4. other functionalities. (entry from Genetic Analysis Software) | genomic analysis, imaging genomics, next generation sequencing, snp, gene, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: wANNOVAR has parent organization: OpenBioinformatics.org |
PMID:20601685 | Free | nlx_154225, biotools:annovar, OMICS_00165 | https://bio.tools/annovar https://bio.tools/annovar |
SCR_012821 | functional ANNOtation of genetic VARiants, ANNOVAR: Functional annotation of genetic variants | 2026-02-15 09:20:40 | 5946 | |||||
|
PerlPrimer Resource Report Resource Website 100+ mentions |
PerlPrimer (RRID:SCR_012038) | software application, software resource | A free, open-source GUI software application written in Perl that designs primers for standard PCR, bisulphite PCR, real-time PCR (QPCR) and sequencing. |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
PMID:15073005 DOI:10.1093/bioinformatics/bth254 |
Open unspecified license | OMICS_02354 | https://sources.debian.org/src/perlprimer/ | SCR_012038 | PerlPrimer - open-source PCR primer design | 2026-02-15 09:20:26 | 236 | |||||||
|
LEfSe Resource Report Resource Website 5000+ mentions |
LEfSe (RRID:SCR_014609) | algorithm resource, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Algorithm for high-dimensional biomarker discovery and explanation that identifies genes, pathways, or taxa characterizing the differences between two or more biological conditions. The algorithm identifies features that are statistically different among biological classes, then performs additional tests to assess whether these differences are consistent with respect to expected biological behavior. Statistical significance and biological relevance are emphasized., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | microbiome, algorithm, biomarker, genomic feature, web application |
is listed by: Human Microbiome Project is listed by: Debian is listed by: OMICtools |
DOI:10.1186/gb-2011-12-6-r60 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_07818 | https://sources.debian.org/src/lefse/ | SCR_014609 | LDA Effect Size | 2026-02-15 09:20:57 | 7008 | ||||||
|
Fastahack Resource Report Resource Website 1+ mentions |
Fastahack (RRID:SCR_016090) | software application, software resource | Software application for indexing and extracting sequences and subsequences from FASTA files. It will only generate indexes for FASTA files in which the sequences have self-consistent line lengths. | extract, quickly, subsequence, sequence, FASTA, files, generate, index |
is listed by: Debian is listed by: OMICtools |
Free, Available for download | OMICS_20516 | https://packages.debian.org/stretch/fastahack https://sources.debian.org/src/fastahack/ |
SCR_016090 | 2026-02-15 09:21:31 | 1 | ||||||||
|
PyNWB Resource Report Resource Website 1+ mentions |
PyNWB (RRID:SCR_017452) | software application, software resource | Software Python package for working with Neurodata stored in Neurodata Without Borders files. Software providing API allowing users to read and create NWB formatted HDF5 files. Developed in support to NWB project with aim of spreading standardized data format for cellular based neurophysiology information. | Neurodata, stored, NWB, file, share, standardized, data, format, neurophysiology, BRAIN Initiative |
uses: Hierarchical Data Modeling Framework is used by: NWB Explorer is recommended by: BRAIN Initiative is listed by: OMICtools is related to: Neurodata Extensions Catalog is related to: HDMF Common Schema is related to: NWB Inspector |
Kavli Foundation ; General Electric ; Howard Hughes Medical Institute ; Allen Institute for Brain Science ; NSF 0855272; International Neuroinformatics Coordinating Facility ; NIH BRAIN Initiative R24 MH116922 |
PMID:26590340 | Free, Available for downloading, Freely available | https://github.com/NeurodataWithoutBorders/pynwb | https://github.com/AllenInstitute/nwb-api | SCR_017452 | 2026-02-15 09:22:02 | 4 | ||||||
|
Ancestrymap Resource Report Resource Website 10+ mentions |
Ancestrymap (RRID:SCR_004353) | ANCESTRYMAP | software application, source code, software resource | Software application that finds skews in ancestry that are potentially associated with disease genes in recently mixed populations like African Americans. It can be downloaded for either UNIX or Linux. | disease gene, ancestry, gene, genomic, unix, linux, admixture mapping, admixture, genome, linkage disequilibrium, population |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools has parent organization: Harvard Medical School; Massachusetts; USA |
Burroughs Wellcome Fund ; NHGRI K-01 HG002758-01 |
PMID:15088269 | Restricted | nlx_39116, biotools:ancestrymap, OMICS_02083 | https://reich.hms.harvard.edu/software https://bio.tools/ancestrymap |
http://genepath.med.harvard.edu/~reich/Software.htm, http://genetics.med.harvard.edu/reich/Reich_Lab/Software.html | SCR_004353 | 2026-02-15 09:18:45 | 12 |
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