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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
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 | 2026-09-19 12:58:12 | 595 | |||||||
|
Bionitio Resource Report Resource Website 1+ mentions |
Bionitio (RRID:SCR_017259) | software resource, software toolkit | Open source software tool to provide template for command line bioinformatics tools in various programming languages. Program reads one or more input FASTA files, computes variety of statistics on each file, and prints tabulated output. Used as basis for learning and as foundation for starting new projects. | template, command, line, bioinformatic, tool, programming, language, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: University of Melbourne; Victoria; Australia |
Free, Available for download, Freely available | biotools:bionitio | https://bio.tools/Bionitio | SCR_017259 | 2026-09-19 12:58:15 | 2 | ||||||||
|
iPiG Resource Report Resource Website |
iPiG (RRID:SCR_016164) | iPiG | software application, software resource, standalone software | Standalone software tool for the integration of peptide identifications from mass spectrometry experiments into existing genome browser visualizations. | integration, peptide, spectrum, match, genome, browser, visualization, experiment, pms, ms, bio.tools |
uses: UCSC Genome Browser is listed by: bio.tools is listed by: Debian |
Robert Koch-Institute | PMID:23226516 DOI:10.1371/journal.pone.0050246 |
Free, Available for download | biotools:ipig, OMICS_06913 | https://bio.tools/ipig, https://sources.debian.org/src/ipig/ | SCR_016164 | iPiG: Integrating Peptide Spectrum Matches Into Genome Browser Visualizations | 2026-09-19 12:58:14 | 0 | ||||
|
Bio2BEL Resource Report Resource Website 1+ mentions |
Bio2BEL (RRID:SCR_017659) | software resource, software toolkit | Software Python package enabling Biological Expression Language to act as semantic integration layer for multi modal and multi scale data sets in life sciences. Used for integrating biological databases and structured data sources in BEL. Has ability to support curation of pathway mappings, integration of pathway databases, and machine learning applications. | Biological, expression, language, integration, layer, dataset, biological, database |
uses: PyBEL is listed by: Debian is listed by: bio.tools is related to: Biological Expression Language |
DOI:10.1101/631812 | Free, Available for download, Freely available | biotools:bio2bEL, BioTools:Bio2BEL | https://github.com/bio2bel/bio2bel, https://bio.tools/Bio2BEL, https://bio.tools/Bio2BEL | SCR_017659 | 2026-09-19 12:58:16 | 7 | |||||||
|
BioBERT Resource Report Resource Website 50+ mentions |
BioBERT (RRID:SCR_017547) | software application, software resource | Pre-trained biomedical language representation model for biomedical text mining. This repository provides fine-tuning codes of BioBERT, language representation model for biomedical domain, especially designed for biomedical text mining tasks such as biomedical named entity recognition, relation extraction, question answering, etc. | Pretrained, biomedical, language, representation, model, text, mining, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: BERT |
National Research Foundation of Korea | DOI:10.1093/bioinformatics/btz682 | Free, Available for download, Freely available | biotools:biobERt | https://github.com/naver/biobert-pretrained, https://bio.tools/BioBERT | SCR_017547 | Bidirectional Encoder Representations from Transformers for Biomedical Text Mining | 2026-09-19 12:58:16 | 56 | |||||
|
MendelIHT.jl Resource Report Resource Website 1+ mentions |
MendelIHT.jl (RRID:SCR_018292) | software application, software resource | Software Julia package that implements iterative hard thresholding as multiple regression model for GWAS. Built-in support for handling PLINK and VCF files, parallel computing, fits a variety of GLM models, and handles grouping/weighting SNPs. | GWAS, iterative hard thresholding, multiple regression, GLM model, feature selection, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: PLINK |
DOI:10.1101/697755 | Free, Available for download, Freely available | biotools:mendeliht.jl | https://bio.tools/mendeliht.jl | SCR_018292 | Mendel Iterative Hard Thresholding.jl, Mendel Iterative Hard Thresholding, MendelIHT | 2026-09-19 12:58:16 | 2 | ||||||
|
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 | 2026-09-19 12:58:17 | 1 | ||||||||
|
BioConda Resource Report Resource Website 50+ mentions |
BioConda (RRID:SCR_018316) | software application, software resource | Software distribution management for life sciences. Channel for Conda package manager specializing in bioinformatics software. Consists of repository of recipes hosted on GitHub, build system turning these recipes into conda packages, repository of packages containing bioinformatics packages ready to use with conda install. | Software distribution management, bioinformatic software, package repository, GitHub, conda, bio.tools |
lists: CCS is listed by: bio.tools is listed by: Debian is related to: Conda is related to: RNAProt |
German Research Foundation ; Intramural Program of the National Institute of Diabetes and Digestive and Kidney Diseases ; Netherlands Organisation for Scientific Research ; NYU Abu Dhabi Research Institute |
PMID:29967506 | Free, Available for download, Freely available | biotools:bioconda | https://bio.tools/bioconda | SCR_018316 | Bioconda | 2026-09-19 12:58:16 | 73 | |||||
|
CorrDrugTumorMSI Resource Report Resource Website 1+ mentions |
CorrDrugTumorMSI (RRID:SCR_018962) | software application, software resource | Software R pipeline to correlate drug distribution with tumor tissue types in mass spectrometry imaging data. | Drug, tumor heterogeneity, mass spectrometry imaging, spatial methods, drug distribution correlation, tumor tissue types, MSI, imaging data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Freely available | biotools:corrdrugtumormsi | https://bio.tools/corrdrugtumormsi | SCR_018962 | 2026-09-19 12:58:17 | 1 | ||||||||
|
Chromosome Scale Assembler Resource Report Resource Website 1+ mentions |
Chromosome Scale Assembler (RRID:SCR_017960) | CSA | software application, software resource | Software pipeline for high-throughput chromosome level vertebrate genome assembly. Pipeline, which after contig assembly performs post assembly improvements by ordering assembly and closing gaps, as well as splitting of low supported regions. | Assembly, chromosome, vertebrate, genome, contig, closing, gap, splitting, low, supported, region, bio.tools |
is listed by: bio.tools is listed by: Debian |
German Research foundation | Free, Available for download, Freely available | biotools:csa2.6 | https://bio.tools/CSA2.6 | SCR_017960 | Chromosome Scale Assembler | 2026-09-19 12:58:16 | 5 | |||||
|
riborex Resource Report Resource Website 1+ mentions |
riborex (RRID:SCR_019104) | software resource, software toolkit | Software R package for identification of differential translation from Ribo-seq data. Computational tool for mapping genome wide differences in translation efficiency. | Ribo-seq data, differential translation, differential translation identification, mapping genome differences, translation efficiency, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Southern California; Los Angeles; USA |
NHGRI R01 HG006015 | PMID:28158331 | Free, Available for download, Freely available | biotools:riborex | https://bio.tools/riborex | SCR_019104 | riborex v2.3.4 | 2026-09-19 12:58:18 | 7 | |||||
|
Tool recommender system in Galaxy Resource Report Resource Website 1+ mentions |
Tool recommender system in Galaxy (RRID:SCR_018491) | software resource, software toolkit | Software developed by analyzing workflows composed by researchers on European Galaxy server, using deep learning approach. Used to recommend tools in Galaxy. Gated recurrent units neural network. | Recommender system, Galaxy, Workflows, Deep learning, Neural networks, Gated recurrent units, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Galaxy |
Free, Freely available | biotools:tool_recommender_system_in_galaxy | https://bio.tools/tool_recommender_system_in_galaxy | SCR_018491 | Galaxy tool recommendation, Tool recommender system in Galaxy using deep learning | 2026-09-19 12:58:17 | 2 | |||||||
|
ADMIXTOOLS Resource Report Resource Website 100+ mentions |
ADMIXTOOLS (RRID:SCR_018495) | software resource, software toolkit | Software package that supports formal tests of whether admixture occurred, and makes it possible to infer admixture proportions and dates. | Formal test support, admixture, infer admixture proportion, infer admixture date, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Harvard University; Cambridge; United States |
NIGMS GM100233; U.S. National Science Foundation HOMINID |
PMID:22960212 | Free, Available for download, Freely available | biotools:admixtools | http://genetics.med.harvard.edu/reich/Reich_Lab/Software.html., https://bio.tools/admixtools | SCR_018495 | 2026-09-19 12:58:17 | 222 | ||||||
|
CITE-seq-Count Resource Report Resource Website 50+ mentions |
CITE-seq-Count (RRID:SCR_019239) | software resource, software toolkit | Software python package that allows to count antibody TAGS from CITE-seq and/or cell hashing experiment. Software tool that allows to get UMI counts from single cell protein assay. Used to count (UMI counts) antibody-derived-tags (ADTs) or Cell Hashing tags (HTOs) in raw sequencing reads and build count matrix. | antibody TAGS count, CITE-seq, cell hashing experiment, antibody derived tags, cell hashing tags, raw sequencing reads, build count matrix, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:https:cite-seq-count | https://cite-seq.com/computational-tools/, https://bio.tools/cite-seq-count | SCR_019239 | CITE-seq-Count v1.4.0, Cellular Indexing of Transcriptomes and Epitopes by Sequencing Count | 2026-09-19 12:58:18 | 60 | |||||||
|
GeCo3 Resource Report Resource Website 1+ mentions |
GeCo3 (RRID:SCR_018877) | software application, software resource | Software tool as DNA compressor that uses neural network to do mixing of experts. | DNA compressor, neural network, expert mixing, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Freely available | biotools:geco3 | https://bio.tools/geco3 | SCR_018877 | 2026-09-19 12:58:17 | 2 | ||||||||
|
BayesEpiModels Resource Report Resource Website 1+ mentions |
BayesEpiModels (RRID:SCR_019291) | software application, software resource | Software tool for accessing performance of different epidemiological models, including both growth and compartmental models, in Bayesian framework. | Stochastic growth model, Stochastic SIR model, Bayesian inference, epidemiological models, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:bayesepimodels | https://bio.tools/bayesepimodels | SCR_019291 | 2026-09-19 12:58:18 | 1 | ||||||||
|
EpiDISH R package Resource Report Resource Website 10+ mentions |
EpiDISH R package (RRID:SCR_018004) | EpiDISH | software resource, software toolkit | Software R package provides tools to infer proportions of priori known cell-types present in sample representing mixture of such cell-types. Comparison of reference based algorithms for correcting cell-type heterogeneity in Epigenome-Wide Association Studies. | Epigenetic, sample heterogeneity, reference, algorithm, correcting, cell type, bio.tools |
is listed by: bio.tools is listed by: Debian |
Chinese Academy of Sciences ; EU-FP7 ; Max-Planck Society ; NSFC 31571359; Royal Society Newton Advanced Fellowship ; Shanghai Institute for Biological Sciences |
PMID:28193155 | Free, Available for download, Freely available | biotools:epidish | https://github.com/sjczheng/EpiDISH, https://bio.tools/epidish | SCR_018004 | Epigenetic Dissection of Intra-Sample Heterogeneity | 2026-09-19 12:58:16 | 14 | ||||
|
Nucleic Acid Database Resource Report Resource Website 10+ mentions |
Nucleic Acid Database (RRID:SCR_003255) | NDB | data or information resource, database | A database of three-dimensional structural information about nucleic acids and their complexes. In addition to primary data, it contains derived geometric data, classifications of structures and motifs, standards for describing nucleic acid features, as well as tools and software for the analysis of nucleic acids. A variety of search capabilities are available, as are many different types of reports. NDB maintains the macromolecular Crystallographic Information File (mmCIF). | nucleic acid, dna, nucleopeptide, nucleoprotein, nucleotide, rna, transfection, sequence, structure, function, bio.tools, FASEB list |
is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: MINAS - Metal Ions in Nucleic AcidS is related to: Biological Magnetic Resonance Data Bank (BMRB) is related to: Jenalib: Jena Library of Biological Macromolecules has parent organization: Rutgers University; New Jersey; USA |
NSF ; DOE ; NIH |
PMID:24185695 PMID:1384741 |
Free, Available for download, Freely available | nif-0000-03184, biotools:ndb, r3d100010415 | https://bio.tools/ndb, https://doi.org/10.17616/R3531R | SCR_003255 | 2026-09-19 12:56:39 | 37 | |||||
|
RefSeq Resource Report Resource Website 10000+ mentions |
RefSeq (RRID:SCR_003496) | data or information resource, database | Collection of curated, non-redundant genomic DNA, transcript RNA, and protein sequences produced by NCBI. Provides a reference for genome annotation, gene identification and characterization, mutation and polymorphism analysis, expression studies, and comparative analyses. Accessed through the Nucleotide and Protein databases. | reference sequence, transcript, protein, dna, rna, plasmid, organelle, virus, genome, nucleic acid, ortholog, paralog, haplotype, nucleotide sequence, gene expression, blast, gold standard, bio.tools |
is listed by: OMICtools is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: BeetleBase is related to: EcoGene is related to: INSDC is related to: HFV Database is related to: RefSeqGene is related to: NCBI Protein Database is related to: RefSeqGene is related to: UniParc at the EBI is related to: NCBI Nucleotide is related to: UniParc is related to: ProRepeat is related to: NCBI Virus is related to: Codon and Codon-Pair Usage Tables is related to: RefSeq non-redundant proteins has parent organization: NCBI |
PMID:24316578 PMID:24259432 PMID:22121212 PMID:18927115 PMID:17130148 PMID:15608248 |
Free, Available for download, Freely available | SCR_016579, nif-0000-03397, OMICS_01659, biotools:refseq, r3d100011306 | ftp://ftp.ncbi.nlm.nih.gov/refseq, https://bio.tools/refseq, https://doi.org/10.17616/R3HP70 | SCR_003496 | RefSeq, , Reference Sequence Database, Reference Sequence, Reference Sequences, NCBI | 2026-09-19 12:56:40 | 19506 | ||||||
|
MutDB Resource Report Resource Website 10+ mentions |
MutDB (RRID:SCR_003251) | data or information resource, database | Database with annotations for human variation data with protein structural information and other functionally relevant information, if available. The mutations are organized by gene. | web database, annotation database, human genome, human protein, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Buck Institute; California; USA |
PMID:15980479 | Free, Freely available | biotools:mutdb, nif-0000-03173 | https://bio.tools/mutdb | SCR_003251 | 2026-09-19 12:56:39 | 10 |
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.
