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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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MP3 tool Resource Report Resource Website 1+ mentions |
MP3 tool (RRID:SCR_019282) | software application, software resource, simulation software | Software tool for prediction of pathogenic proteins in genomic and metagenomic data. Used for identification of partial pathogenic proteins predicted from short (100-150 bp) metagenomic reads and also performs on complete protein sequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | pathogenic proteins, pathogenic proteins prediction, genomic data, metagenomic data, partial pathogenic proteins, partial pathogenic proteins prediction, complete protein sequences, bio.tools |
is listed by: bio.tools is listed by: Debian |
Institutional Research Fund of IISER Bhopal | PMID:24736651 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:mp3 | https://bio.tools/mp3 | SCR_019282 | MP3 | 2026-02-16 09:49:42 | 2 | |||||
|
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 | |||||
|
ALCHEMY Resource Report Resource Website 1+ mentions |
ALCHEMY (RRID:SCR_005761) | ALCHEMY | source code, software resource | ALCHEMY is a genotype calling algorithm for Affymetrix and Illumina products which is not based on clustering methods. Features include explicit handling of reduced heterozygosity due to inbreeding and accurate results with small sample sizes. ALCHEMY is a method for automated calling of diploid genotypes from raw intensity data produced by various high-throughput multiplexed SNP genotyping methods. It has been developed for and tested on Affymetrix GeneChip Arrays, Illumina GoldenGate, and Illumina Infinium based assays. Primary motivations for ALCHEMY''s development was the lack of available genotype calling methods which can perform well in the absence of heterozygous samples (due to panels of inbred lines being genotyped) or provide accurate calls with small sample batches. ALCHEMY differs from other genotype calling methods in that genotype inference is based on a parametric Bayesian model of the raw intensity data rather than a generalized clustering approach and the model incorporates population genetic principles such as Hardy-Weinberg equilibrium adjusted for inbreeding levels. ALCHEMY can simultaneously estimate individual sample inbreeding coefficients from the data and use them to improve statistical inference of diploid genotypes at individual SNPs. The main documentation for ALCHEMY is maintained on the sourceforge-hosted MediaWiki system. Features * Population genetic model based SNP genotype calling * Simultaneous estimation of per-sample inbreeding coefficients, allele frequencies, and genotypes * Bayesian model provides posterior probabilities of genotype correctness as quality measures * Growing number of scripts and supporting programs for validation of genotypes against control data and output reformating needs * Multithreaded program for parallel execution on multi-CPU/core systems * Non-clustering based methods can handle small sample sets for empirical optimization of sample preparation techniques and accurate calling of SNPs missing genotype classes ALCHEMY is written in C and developed on the GNU/Linux platform. It should compile on any current GNU/Linux distribution with the development packages for the GNU Scientific Library (gsl) and other development packages for standard system libraries. It may also compile and run on Mac OS X if gsl is installed. | diploid, genotype, snp, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: SourceForge has parent organization: Cornell University; New York; USA |
NSF 0606461 | PMID:20926420 | GNU General Public License | biotools:alchemy, nlx_149227 | https://bio.tools/alchemy | SCR_005761 | ALCHEMY - An automated population genetic model driven SNP genotype calling method | 2026-02-15 09:19:11 | 5 | ||||
|
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 | ||||||
|
RNAplex Resource Report Resource Website 10+ mentions |
RNAplex (RRID:SCR_002763) | RNAplex | source code, software resource | Software tool to rapidly search for short interactions between two long RNAs. | interaction, rna, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Leipzig; Saxony; Germany |
PMID:21593134 PMID:18434344 |
Free, Freely available, Available for download | rid_000107, biotools:rnaplex | https://bio.tools/rnaplex | SCR_002763 | 2026-02-15 09:18:22 | 37 | ||||||
|
TomoMiner Resource Report Resource Website 1+ mentions |
TomoMiner (RRID:SCR_015045) | source code, software resource | Software platform for large-scale cryo electron subtomogram classification, alignment, and averaging. | analysis platform, cryo electron subtomogram, subtomogram classification, subtomogram alignment, subtomogram averaging, subtomogram analysis, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Southern California; Los Angeles; USA requires: Python Programming Language requires: NumPy requires: SciPy requires: LAPACK linear algebra library requires: Cython C-Extensions for Python |
Available for download | biotools:tomominer | https://bio.tools/tomominer | SCR_015045 | 2026-02-15 09:21:05 | 3 | ||||||||
|
Human Gene Mutation Database Resource Report Resource Website 1000+ mentions |
Human Gene Mutation Database (RRID:SCR_001621) | HGMD | data or information resource, database | Curated database of known (published) gene lesions responsible for human inherited disease. | gene, disease, gene lesion, mutation, deletion, insertion, duplication, rearrangement, nuclear gene, functional polymorphism, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: BIOBASE Corporation has parent organization: Cardiff University; Wales; United Kingdom |
Inherited disease | PMID:22948725 PMID:20368137 PMID:20038494 PMID:19348700 PMID:18428754 PMID:18245393 PMID:12754702 PMID:10612821 PMID:9399854 PMID:9066272 PMID:8882888 |
Free, Freely available | nlx_153887, SCR_001888, biotools:hgmd, nif-0000-10459, OMICS_00281 | http://www.hgmd.cf.ac.uk/ac/index.php https://bio.tools/hgmd |
SCR_001621 | The Human Gene Mutation Database, The Human Gene Mutation Database at the Institute of Medical Genetics in Cardiff | 2026-02-16 09:45:33 | 2462 | ||||
|
Identifiers.org Resource Report Resource Website 50+ mentions |
Identifiers.org (RRID:SCR_003735) | Identifiers.org | production service resource, service resource, identifier resolution | A system providing resolvable persistent Uniform Resource Identifiers (URIs) used to identify data for the scientific community, with a current focus on the Life Sciences domain. The provision of resolvable identifiers (URLs) fits well with the Semantic Web vision, and the Linked Data initiative. It provides direct access to the identified data using one chosen physical location (or resource). If more than one physical locations providing the data are recorded in the Registry, then you can access them via the top banner or by using a profile. | identifier, life sciences, bio.tools |
uses: MIRIAM Resources is listed by: bio.tools is listed by: Debian has parent organization: European Bioinformatics Institute |
Free | nlx_157931, biotools:identifiers.org | https://bio.tools/identifiers.org | SCR_003735 | 2026-02-16 09:46:06 | 50 | |||||||
|
circlize Resource Report Resource Website 1000+ mentions |
circlize (RRID:SCR_002141) | software application, software resource, standalone software | Software package that implements and enhances circular visualization in R. Due to natural born feature of R to draw statistical graphics, this package can provide more general and flexible way to visualize huge information in circular style. | circular visualization, draw statistical graphics, circular style graphics, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: CRAN |
PMID:24930139 | Free, Available for download, Freely available | OMICS_04658, biotools:circlize | https://github.com/jokergoo/circlize https://bio.tools/circlize |
SCR_002141 | circlize: Circular Visualization in R | 2026-02-16 09:45:39 | 1073 | ||||||
|
NGSUtils Resource Report Resource Website 10+ mentions |
NGSUtils (RRID:SCR_001236) | NGSUtils | software resource, software toolkit | A suite of software tools for analyzing and manipulating next-generation sequencing datasets, such as FASTQ, BED and BAM format files. These tools provide a stable and modular platform for data management and analysis. | mac os x, linux, next-generation sequencing, illumia, solid, 454, ion torrent, pac bio, sequencing, dna resequcing, rna resequcing, chip-seq, clip-seq, targeted resequencing, agilent exome capture, pcr targeting, dna, rna, mapping pipeline, python, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Indiana University School of Medicine; Indiana; USA |
PMID:23314324 | Free, Available for download, Freely available | biotools:ngsutils, OMICS_02104 | https://bio.tools/ngsutils | SCR_001236 | NGSUtils - Tools for next-generation sequencing analysis | 2026-02-16 09:45:26 | 38 | |||||
|
khmer Resource Report Resource Website 10+ mentions |
khmer (RRID:SCR_001156) | software resource, software toolkit | Software library and suite of command line tools for working with DNA sequence that takes a k-mer-centric approach to sequence analysis. It is primarily aimed at short-read sequencing data such as that produced by the Illumina platform. | dna sequence, short-read, sequencing, dna, illumina, sequence analysis, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
NHGRI R01HG007513 | PMID:26535114 DOI:10.12688/f1000research.6924.1 |
Free, Available for download, Freely available | SciRes_000166, OMICS_02560, biotools:khmer | https://github.com/dib-lab/khmer https://bio.tools/khmer https://sources.debian.org/src/khmer/ |
https://github.com/ged-lab/khmer, http://ged.msu.edu/papers/2012-diginorm/ | SCR_001156 | khmer project, khmer - k-mer counting & filtering FTW, khmer - k-mer counting and filtering FTW, khmer: k-mer counting filtering and graph traversal FTW | 2026-02-16 09:45:25 | 25 | ||||
|
nondetects Resource Report Resource Website 1+ mentions |
nondetects (RRID:SCR_001702) | software application, software resource, standalone software | Software R package to model and impute non-detects in results of qPCR experiments.Used to directly model non-detects as missing data. | mac os x, unix/linux, windows, r, assay domain, gene expression, preprocessing, technology, workflow step, qpcr, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
NCI CA009363; NCI CA138249; NHGRI HG006853; Edelman-Gardner Foundation |
PMID:24764462 | Free, Available for download, Freely available | OMICS_03938, biotools:nondetects | https://bio.tools/nondetects | SCR_001702 | nondetects - Non-detects in qPCR data | 2026-02-16 09:45:33 | 1 | |||||
|
pRESTO Resource Report Resource Website 50+ mentions |
pRESTO (RRID:SCR_001782) | pRESTO | software resource, software toolkit | Software toolkit for processing raw reads from high-throughput sequencing of lymphocyte repertoires. | lymphocyte, high throughput sequencing, processing, raw reads, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Yale School of Medicine; Connecticut; USA |
EMD/Merck/Serono ; United States-Israel Binational Science Foundation 2009046; NCRR RR19895; NLM T15 LM07056; NIAAA U19AI089992; NIAAA U19AI050864 |
PMID:24618469 | Free, Freely available | SCR_001782 | REpertoire Sequencing TOolkit | 2026-02-16 09:45:35 | 70 | ||||||
|
MAKER Resource Report Resource Website 1000+ mentions |
MAKER (RRID:SCR_005309) | software resource, software toolkit | Software genome annotation pipeline. Portable and easily configurable genome annotation pipeline. Used to allow smaller eukaryotic and prokaryotic genomeprojects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence based quality values. | gene prediction, genome annotation, identifies repeats, aligns ESTs and proteins to genome, data management, genome annotation, annotation, curation, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is related to: MAKER Web Annotation Service has parent organization: University of Utah; Utah; USA |
PMID:25501943 | SCR_023883, nlx_144363, biotools:maker | https://bio.tools/maker https://github.com/Yandell-Lab/maker |
SCR_005309 | Maker2, maker | 2026-02-16 09:46:27 | 1422 | |||||||
|
Unipro UGENE Resource Report Resource Website 100+ mentions |
Unipro UGENE (RRID:SCR_005579) | UGENE | software resource, software toolkit | A multiplatform open-source software to assist molecular biologists without much expertise in bioinformatics to manage, analyze and visualize their data. UGENE integrates widely used bioinformatics tools within a common user interface. The toolkit supports multiple biological data formats and allows the retrieval of data from remote data sources. It provides visualization modules for biological objects such as annotated genome sequences, Next Generation Sequencing (NGS) assembly data, multiple sequence alignments, phylogenetic trees and 3D structures. Most of the integrated algorithms are tuned for maximum performance by the usage of multithreading and special processor instructions. UGENE includes a visual environment for creating reusable workflows that can be launched on local resources or in a High Performance Computing (HPC) environment. UGENE is written in C++ using the Qt framework. The built-in plugin system and structured UGENE API make it possible to extend the toolkit with new functionality. | c++, windows, mac os, linux, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:22368248 DOI:10.1093/bioinformatics/bts091 |
GNU General Public License, v2, Acknowledgement requested | OMICS_01022, biotools:ugene | https://bio.tools/ugene https://sources.debian.org/src/ugene/ |
SCR_005579 | 2026-02-16 09:46:29 | 170 | ||||||
|
PoolHap Resource Report Resource Website |
PoolHap (RRID:SCR_012129) | software application, software resource, standalone software | Software tool for inferring haplotypes from pooled sequencing. Enables to infer strain numbers and haplotype frequencies in silico from sequences of pooled samples. | inferring haplotypes, pooled sequencing, haplotype frequencies, infer strain numbers, pooled samples sequences, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
PMID:21264334 | Free, Available for download, Freely available | biotools:poolhap, OMICS_05832 | https://bio.tools/poolhap | SCR_012129 | Inferring Haplotype frequencies from Pooled sequencing, poolhap2, PoolHap2 | 2026-02-16 09:48:04 | 0 | ||||||
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imDEV Resource Report Resource Website 1+ mentions |
imDEV (RRID:SCR_014674) | software application, software resource, systems interoperability software | A software application of RExcel that integrates R into Excel as an embedded additon for omics tasks and analysis. It can be used specifically for tasks concerning multivariate data visualization, exploration, and analysis. imDev has interactive modules for dimensional reduction, prediction, feature selection, analysis of correlation, and generation of networked structures, all of which provide an integrated environment for systems level analysis of multivariate data. | statistical analysis, statistical analysis package, r, r package, excel, data visualization, feature selection, omics, systems interoperability, software, metabolomics, bio.tools |
is listed by: Metabolomics Workbench is listed by: Debian is listed by: bio.tools |
DOI:10.1093/bioinformatics/bts439 | Supports Microsoft Excel versions 2003-2010 | biotools:imdev | https://sourceforge.net/projects/imdev/ https://bio.tools/imdev |
SCR_014674 | Interactive modules for Data Exploration and Visualization, Interactive modules for Data Exploration and Visualization (imDEV) | 2026-02-16 09:48:36 | 8 | ||||||
|
Protein Prospector Resource Report Resource Website 500+ mentions |
Protein Prospector (RRID:SCR_014558) | software resource, software toolkit | A package of over twenty mass spectrometry-based tools primarily geared toward proteomic data analysis and database mining. It can be run from the command line, but is primarily used through a web browser, and there is a public website that allows anyone to use the software without local installation. Tandem mass spectrometry analysis tools are used for database searching and identification of peptides, including post-translationally modified peptides and cross-linked peptides. Support for isotope and label-free quantification from this type of data is provided. MS-Viewer software allows sharing and displaying of annotated spectra from many different tandem mass spectrometry data analysis packages. Other tools include software for analyzing peptide mass fingerprinting data (MS-Fit); prediction of theoretical fragmentation of peptides (MS-Product); theoretical chemical or enzymatic digestion of proteins (MS-Digest); and theoretical modeling of the isotope distribution of any chemical, including peptides (MS-Isotope). Searches using amino acid sequence can be used to identify homologous peptides in a database (MS-Pattern); the use of the combination of amino acid sequence and masses can be used for homologous peptide and protein identification using MS-Homology. Tandem mass spectrometry peak list files can be filtered for the presence of certain peaks or neutral losses using MS-Filter. Given a list of proteins, MS-Bridge can report all potential cross-linked peptide combinations of a specified mass. Given a precursor peptide mass and information about known amino acid presence, absence, or modifications, MS-Comp can report all amino acid combinations that could lead to the observed mass. | database search program, database search, database management, peptide, protein, mass spectrometry, ms, utility program, batch msms, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: University of California at San Francisco; California; USA |
Open source, Freely available to academic researchers | biotools:proteinprospector | https://bio.tools/proteinprospector | SCR_014558 | ProteinProspector | 2026-02-16 09:48:38 | 569 | |||||||
|
PhaseME Resource Report Resource Website 1+ mentions |
PhaseME (RRID:SCR_018739) | software resource, software toolkit | Software tool set to assess quality of per read phasing information and help to reduce errors during this process. | Variant Call Format Tools, quality assessment, read phasing, error, reduce error, read phasing information, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:phaseme | https://bio.tools/phaseme/ | SCR_018739 | 2026-02-16 09:49:34 | 1 |
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