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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
SAMTOOLS Resource Report Resource Website 10000+ mentions |
SAMTOOLS (RRID:SCR_002105) | SAMtools | sequence analysis software, data processing software, data analysis software, software toolkit, software application, software resource | Original SAMTOOLS package has been split into three separate repositories including Samtools, BCFtools and HTSlib. Samtools for manipulating next generation sequencing data used for reading, writing, editing, indexing,viewing nucleotide alignments in SAM,BAM,CRAM format. BCFtools used for reading, writing BCF2,VCF, gVCF files and calling, filtering, summarising SNP and short indel sequence variants. HTSlib used for reading, writing high throughput sequencing data. | Samtools, BCFtools, HTSlib, next generation sequencing, nucleotide alignments, sequence variant, genomic, c, perl, read, alignment, nucleotide, sequence, data, process, sam, bam, cram, vcf, bcf, bio.tools |
is used by: deFuse is used by: Short Read Sequence Typing for Bacterial Pathogens is used by: ROSE is used by: Fcirc is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: SNVer is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: Platypus is related to: shovill is related to: pysam has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom is parent organization of: SAMtools/BCFtools is required by: RelocaTE is required by: Wessim is required by: SL-quant is required by: smMIPfil |
Wellcome Trust ; NHGRI U54 HG002750 |
PMID:19505943 PMID:21903627 DOI:10.1093/bioinformatics/btp352 |
Free, Available for download, Freely available | SCR_018682, biotools:samtools, OMICS_01074, nlx_154607, OMICS_00090 | https://github.com/samtools/samtools https://github.com/samtools/htslib https://bio.tools/samtools https://sources.debian.org/src/samtools/ |
http://samtools.sourceforge.net/ | SCR_002105 | samtools, Samtools, Sequence Alignment Map TOOLS, SAMtools, SAM tools | 2026-02-14 02:00:18 | 30156 | |||
|
DWGSIM Resource Report Resource Website 50+ mentions |
DWGSIM (RRID:SCR_002342) | DWGSIM | software resource | Whole Genome Simulator for Next-Generation Sequencing. | next-generation sequencing, whole genome simulation |
is listed by: OMICtools is listed by: Debian |
GNU General Public License, v2 | OMICS_00249 | https://sources.debian.org/src/dwgsim/ | SCR_002342 | 2026-02-14 02:00:23 | 51 | |||||||
|
BEETL-fastq Resource Report Resource Website |
BEETL-fastq (RRID:SCR_002341) | software resource | Software tool that not only compresses FASTQ-formatted DNA reads more compactly than gzip but also permits rapid search for k-mer queries within the archived sequences. The full FASTQ record of each matching read or read pair is returned, allowing the search results to be piped directly to any of the many standard tools that accept FASTQ data as input. Searchable compressed archive for DNA reads. | Searchable compressed archive, DNA reads, compresses FASTQ-formatted DNA reads, bio.tools, |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Burrows-Wheeler transform |
PMID:24950811 | Free, Available for download, Freely available | OMICS_04900, biotools:beetl | https://bio.tools/beetl | SCR_002341 | 2026-02-14 02:00:16 | 0 | |||||||
|
Blood Group Antigen Gene Mutation Database Resource Report Resource Website |
Blood Group Antigen Gene Mutation Database (RRID:SCR_002297) | BGMUT | data repository, storage service resource, data or information resource, service resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 23, 2019.BGMUT was database that provided publicly accessible platform for DNA sequences and curated set of blood mutation information. Data Archive are available at ftp://ftp.ncbi.nlm.nih.gov/pub/mhc/rbc/Final Archive. | blood, gene, genetic, allele, allelic, alteration, antigen, blood group, human, mutation, genetic variation, non-human animal, orthologous gene, orthologue, phenotype, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: NCBI dbRBC has parent organization: Albert Einstein College of Medicine; New York; USA has parent organization: Roswell Park Cancer Institute has parent organization: Medical University of Graz; Graz; Austria has parent organization: Human Genome Variation Society |
Albert Einstein College of Medicine; New York; USA ; David Opochinsky/Blumenfeld Family Fund ; NIH |
PMID:22084196 | THIS RESOURCE IS NO LONGER IN SERVICE. | nif-0000-21064, biotools:bgmut | https://bio.tools/bgmut | http://www.bioc.aecom.yu.edu/bgmut/index.htm, http://www.ncbi.nlm.nih.gov/projects/gv/rbc/xslcgi.fcgi?cmd=bgmut | SCR_002297 | Blood Group Antigen Gene Mutation Database (BGMUT), BGMUT - Blood Group Antigen Gene Mutation Database | 2026-02-14 02:00:22 | 0 | |||
|
DNA DataBank of Japan (DDBJ) Resource Report Resource Website 500+ mentions |
DNA DataBank of Japan (DDBJ) (RRID:SCR_002359) | DDBJ | data repository, storage service resource, data or information resource, service resource, database | Maintains and provides archival, retrieval and analytical resources for biological information. Central DDBJ resource consists of public, open-access nucleotide sequence databases including raw sequence reads, assembly information and functional annotation. Database content is exchanged with EBI and NCBI within the framework of the International Nucleotide Sequence Database Collaboration (INSDC). In 2011, DDBJ launched two new resources: DDBJ Omics Archive and BioProject. DOR is archival database of functional genomics data generated by microarray and highly parallel new generation sequencers. Data are exchanged between the ArrayExpress at EBI and DOR in the common MAGE-TAB format. BioProject provides organizational framework to access metadata about research projects and data from projects that are deposited into different databases. | nucleotide sequence, genome, dna, dna database, dna research, nucleotide, phylogenetics, protein, sequence, protein binding, gene expression, gene, genetics, nucleoid, genomics, protein binding, gold standard, bio.tools, FASEB list |
is recommended by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: OMICtools is listed by: re3data.org is listed by: Debian is listed by: bio.tools is related to: INSDC is related to: GenBank is related to: INSDC is related to: European Nucleotide Archive (ENA) is related to: GenBank is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: Worldwide Protein Data Bank (wwPDB) is related to: Biological Magnetic Resonance Data Bank (BMRB) is related to: PDBe - Protein Data Bank in Europe is related to: PDBe - Protein Data Bank in Europe is related to: European Nucleotide Archive (ENA) is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: NCBI Assembly Archive Viewer has parent organization: National Institute of Genetics; Shizuoka; Japan is parent organization of: DDBJ Omics Archive is parent organization of: BodyMap-Xs is parent organization of: DDBJ Sequence Read Archive is parent organization of: CIBEX: Center for Information Biology gene EXpression database is parent organization of: Japanese Genotype-phenotype Archive (JGA) |
Japanese Ministry of Education Culture Sports Science and Technology MEXT | PMID:26578571 PMID:25477381 |
Free, Freely available, | OMICS_01644, biotools:ddbj, nif-0000-02740, r3d100010218 | https://bio.tools/ddbj https://doi.org/10.17616/R3M01R |
SCR_002359 | DNA DataBank of Japan (DDBJ), DNA DataBank of Japan, DDBJ, DNA Data Bank of Japan, DDBJ - DNA Data Bank of Japan | 2026-02-14 02:00:16 | 627 | ||||
|
PySurfer Resource Report Resource Website 10+ mentions |
PySurfer (RRID:SCR_002524) | PySurfer | data visualization software, data processing software, software library, software toolkit, software application, software resource | Software Python tool for visualization and interaction with cortical surface representations of neuroimaging data from Freesurfer. It extends Mayavi powerful visualization engine with interface for working with MRI and MEG data. PySurfer offers command-line interface designed to broadly replicate Freesurfer program as well as Python library for writing scripts to explore complex datasets., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | eeg, meg, electrocorticography, magnetic resonance, mri, python, neuroimaging |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is related to: FreeSurfer |
Free, Available for download, Freely available | nlx_155930 | http://www.nitrc.org/projects/pysurfer https://sources.debian.org/src/python3-surfer/ |
SCR_002524 | 2026-02-14 02:00:25 | 29 | |||||||
|
ShotGun Resource Report Resource Website 10+ mentions |
ShotGun (RRID:SCR_002529) | sequence analysis software, data processing software, data analysis software, software application, software resource, simulation software | Software for short read simulating in order to facilitate sequencing-based study designs. | sequence based study design, short read stimulation, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
PMID:23357921 | Free, Available for download, Freely available | biotools:abcd, OMICS_00255 | https://bio.tools/abcd | SCR_002529 | ShotGun: a Flexible Short Read Simulator to Facilitate Sequencing-based Study Designs | 2026-02-14 02:00:26 | 32 | ||||||
|
Gibbs Motif Sampler Resource Report Resource Website 1+ mentions |
Gibbs Motif Sampler (RRID:SCR_002550) | Gibbs Motif Sampler | data analysis service, analysis service resource, production service resource, service resource, software resource | Software to identify motifs, conserved regions, in DNA or protein sequences. | dna, protein, motif, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:gibbs_motif_sampler, OMICS_00496 | https://bio.tools/gibbs_motif_sampler | SCR_002550 | The Gibbs Motif Sampler | 2026-02-14 02:00:17 | 2 | ||||||
|
pymzML Resource Report Resource Website 10+ mentions |
pymzML (RRID:SCR_002500) | software resource | Python module to parse mzML data in Python based on cElementTree. It is an extension to Python that offers (i) an easy access to mass spectrometry (MS) data that allows the rapid development of tools, (ii) a very fast parser for mzML data and (iii) a set of functions to compare or handle spectra., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | standalone software, python, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: mzML has parent organization: University of Munster; North Rhine-Westphalia; Germany |
PMID:22302572 | Free, Available for download, Freely available | biotools:pymzml, OMICS_03355 | https://bio.tools/pymzml | SCR_002500 | 2026-02-14 02:00:17 | 18 | |||||||
|
discoSnp Resource Report Resource Website 1+ mentions |
discoSnp (RRID:SCR_002612) | sequence analysis software, data processing software, data analysis software, software application, software resource | Software designed for discovering Single Nucleotide Polymorphism (SNP) from raw sets of reads obtained with Next Generation Sequencers (NGS). | single nucleotide polymorphism, snp discovery, discover snp, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
SOFIPROTEOL under the FASO project PEAPOL ; INRIA ANR-12-BS02-0008 |
PMID:25404127 | Free, Freely available | biotools:discosnp, OMICS_00267 | https://bio.tools/discosnp https://sources.debian.org/src/discosnp/ |
SCR_002612 | DiscoSnp++, discovering Single Nucleotide Polymorphism, discovering Single Nucleotide Polymorphism (discoSNP) | 2026-02-14 02:00:25 | 9 | |||||
|
IMEx - The International Molecular Exchange Consortium Resource Report Resource Website 100+ mentions |
IMEx - The International Molecular Exchange Consortium (RRID:SCR_002805) | IMEx | data repository, storage service resource, community building portal, portal, consortium, data or information resource, organization portal, service resource, database | Interaction database from international collaboration between major public interaction data providers who share curation effort and develop set of curation rules when capturing data from both directly deposited interaction data or from publications in peer reviewed journals. Performs complete curation of all protein-protein interactions experimentally demonstrated within publication and makes them available in single search interface on common website. Provides data in standards compliant download formats. IMEx partners produce their own separate resources, which range from all encompassing molecular interaction databases, such as are maintained by IntAct, MINT and DIP, organism-centric resources such as BioGrid or MPIDB or biological domain centric, such as MatrixDB. They have committed to making records available, via PSICQUIC webservice, which have been curated to IMEx rules and are available to users as single, non-redundant set of curated publications which can be searched at the IMEx website. Data is made available in standards-compliant tab-deliminated and XML formats, enabling to visualize data using wide range of tools. Consortium is open to participation of additional partners and encourages deposition of data, prior to publication, and will supply unique accession numbers which may be referenced within final article. Submitters may send their data directly to any of member databases using variety of formats, but should conform to guidelines as to minimum information required to describe data. | protein-protein interaction, nonredundant, protein interaction, interaction, proteomics, metadata standard, short course, molecular interaction, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is affiliated with: MINT is related to: MatrixDB is related to: MPIDB is related to: Database of Interacting Proteins (DIP) is related to: Database of Interacting Proteins (DIP) is related to: InnateDB is related to: IntAct is related to: Interaction Reference Index is related to: MPIDB is related to: UniProt is related to: InnateDB is related to: MatrixDB is related to: Biological General Repository for Interaction Datasets (BioGRID) is related to: I2D is related to: Molecular Connections NetPro is related to: SIB Swiss Institute of Bioinformatics is related to: IntAct is related to: PSI-MI is related to: PSICQUIC Registry is related to: mentha is related to: Bioconductor has parent organization: European Bioinformatics Institute works with: CellPhoneDB works with: Cytoscape works with: IntAct works with: MINT works with: MPact: Representation of Interaction Data at MIPS works with: Molecular Connections NetPro works with: Biological General Repository for Interaction Datasets (BioGRID) works with: InnateDB works with: BIND |
European Union | PMID:22453911 PMID:17893861 |
Free, Freely available, Available for download | nif-0000-00447, OMICS_01545, r3d100010669, biotools:imex | http://imex.sourceforge.net/ https://bio.tools/imex https://doi.org/10.17616/R3090W |
SCR_002805 | The International Molecular Exchange Consortium, International Molecular Exchange Consortium | 2026-02-14 02:00:27 | 144 | ||||
|
sapFinder Resource Report Resource Website |
sapFinder (RRID:SCR_002685) | software resource | An R software package, for detection of the variant peptides based on tandem mass spectrometry (MS/MS)-based proteomics data. It automates (1) variation-associated database construction, (2) database searching, (3) post-processing, (4) HTML-based report generation in shotgun proteomics. | standalone software, r, mass spectrometry, proteomics, rna-seq, report writing, snp, visualization, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:25053745 | Free, Available for download, Freely available | biotools:sapfinder, OMICS_05285 | https://bio.tools/sapfinder | SCR_002685 | sapFinder - A package for variant peptides detection and visualization in shotgun proteomics. | 2026-02-14 02:00:26 | 0 | ||||||
|
leeHom Resource Report Resource Website 50+ mentions |
leeHom (RRID:SCR_002710) | software resource | Software program for the Bayesian reconstruction of ancient DNA fragments. The algorithm removes the adaptors and reconstructs the original DNA sequences using a Bayesian maximum a posteriori probability approach. | standalone software, illumina, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:25100869 | Free, Available for download, Freely available | biotools:leehom, OMICS_05254 | https://bio.tools/leehom | SCR_002710 | 2026-02-14 02:00:26 | 53 | |||||||
|
ANDES Resource Report Resource Website 10+ mentions |
ANDES (RRID:SCR_002791) | data processing software, data analysis software, software toolkit, software application, software resource | Software library and a suite of applications, written in Perl and R, for deep sequencing statistical analyses. | deep sequencing, biomarker detection, statistical analysis, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:20633290 | Free, Freely available, Available for download | biotools:andes, OMICS_01119 | https://bio.tools/andes | SCR_002791 | Statistical tools for the Analyses of Deep Sequencing (ANDES), Statistical tools for the Analyses of Deep Sequencing, Statistical tools for the ANalyses of Deep Sequencing | 2026-02-14 02:00:32 | 25 | ||||||
|
NCBI database of Genotypes and Phenotypes (dbGap) Resource Report Resource Website 500+ mentions |
NCBI database of Genotypes and Phenotypes (dbGap) (RRID:SCR_002709) | dbGaP | data repository, storage service resource, data or information resource, service resource, database | Database developed to archive and distribute clinical data and results from studies that have investigated interaction of genotype and phenotype in humans. Database to archive and distribute results of studies including genome-wide association studies, medical sequencing, molecular diagnostic assays, and association between genotype and non-clinical traits. | clinical, trial, genotype, interaction, homology, cell, morphology, interaction, phenotype, molecular diagnosis, genetic recombination, gold standard, bio.tools |
is used by: International Genomics of Alzheimers Project is used by: NIDDK Inflammatory Bowel Disease Genetics Consortium is used by: NIH Heal Project is used by: Genomic Data Commons Data Portal (GDC Data Portal) is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: OMICtools is listed by: re3data.org is listed by: NIDDK Information Network (dkNET) is listed by: bio.tools is listed by: Debian is related to: NIDDK Central Repository is related to: eMERGE Network: electronic Medical Records and Genomics is related to: Framingham Heart Study is related to: PhenoExplorer is related to: Chronic Renal Insufficiency Cohort Study is related to: DbGaP Cleaner is related to: Psychiatric Genomics Consortium is related to: ISCA Consortium is related to: Allen Institute for Brain Science has parent organization: NCBI is parent organization of: Resource for Genetic Epidemiology Research on Adult Health and Aging |
NLM | PMID:24297256 PMID:17898773 |
Restricted | nif-0000-23342, OMICS_00263, biotools:dbgap, r3d100010788 | http://www.ncbi.nlm.nih.gov/sites/entrez?db=gap https://bio.tools/dbgap https://doi.org/10.17616/R3GS4K |
SCR_002709 | database of Genotypes and Phenotypes (dbGaP), dbGaP, NCBI, Database of Genotypes and Phenotypes | 2026-02-14 02:00:30 | 683 | ||||
|
Pathview Resource Report Resource Website 500+ mentions |
Pathview (RRID:SCR_002732) | software resource | A tool set for pathway-based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs. All users need is to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, Pathview also seamlessly integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis. | software package, r, differential expression, gene expression, gene set enrichment, genetics, graph, network, metabolomics, microarray, pathway, proteomics, rna-seq, sequencing, systems biology, visualization, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:23740750 | Free, Freely available, Available for download | biotools:pathview, OMICS_05212 | http://pathview.r-forge.r-project.org/ https://bio.tools/pathview |
SCR_002732 | path view | 2026-02-14 02:00:30 | 520 | ||||||
|
SuperPred: Drug classification and target prediction Resource Report Resource Website |
SuperPred: Drug classification and target prediction (RRID:SCR_002691) | SuperPred | web service, data or information resource, data access protocol, software resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 24,2025. Publicly available web-server to predict medical indication areas based on properties and similarity of chemical compounds. The web-server translates a user-defined molecule into a structural fingerprint that is compared to about 6300 drugs, which are enriched by 7300 links to molecular targets of the drugs, derived through text mining followed by manual curation. Links to the affected pathways are provided. The similarity to the medical compounds is expressed by the Tanimoto coefficient that gives the structural similarity of two compounds. A similarity score higher than 0.85 results in correct ATC prediction for 81% of all cases. As the biological effect is well predictable, if the structural similarity is sufficient, the web-server allows prognoses about the medical indication area of novel compounds and to find new leads for known targets. The combination of physicochemical property and similarity searching provides the possibility to detect new biologically active compounds and novel targets for drug-like compounds. SuperPred can be applied for drug repositioning purposes, too. A further intention of SuperPred is to find side effects elicited by drugs caused through off-target hits. | drug, drug class, drug target, addiction, anatomical therapeutic chemical, application area, biological activity, chemical, chemical classification, chemical property, classification, compound, molecular target, molecule, nervous system, pathway, pharmacological property, physicochemical property, prediction, activity spectra, substance, structural similarity, structure, tanimoto coefficient, tanimoto score, target prediction, target-prediction server, therapeutic approach, therapeutic property, drug classification, target prediction, similarity score, target, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Charite - Universitatsmedizin Berlin; Berlin; Germany |
SFB 449 ; IRTG Berlin-Boston-Kyoto and Deutsche Krebshilfe. ; DFG |
PMID:18499712 PMID:24878925 |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:superpred, nif-0000-00415 | https://bio.tools/superpred | SCR_002691 | 2026-02-14 02:00:29 | 0 | |||||
|
Rainbow Resource Report Resource Website 10+ mentions |
Rainbow (RRID:SCR_002724) | sequence analysis software, data processing software, data analysis software, software application, software resource | Software developed to provide an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq. | software, tool, clustering, assembling, short, read, restriction, site, DNA, sequence, analysis, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:22942077 DOI:10.1093/bioinformatics/bts482 |
Free, Freely available, Available for download | SCR_015992, OMICS_03722, biotools:rainbow | https://bio.tools/rainbow https://sources.debian.org/src/bio-rainbow/ |
SCR_002724 | RAD-seq: Restriction-site Associated DNA sequencing, Bio-rainbow, RAD-seq | 2026-02-14 02:00:30 | 41 | ||||||
|
Coding Potential Calculator Resource Report Resource Website 100+ mentions |
Coding Potential Calculator (RRID:SCR_002764) | CPC | data analysis service, analysis service resource, production service resource, service resource, software resource | A Support Vector Machine-based classifier to assesses the protein-coding potential of a transcript based on six biologically meaningful sequence features. CPC can discriminate coding from noncoding transcripts with high accuracy and speed. In addition to predicting the coding potential of the input transcripts, the CPC web server also graphically displays detailed sequence features and additional annotations of the transcript that may facilitate users' further investigation. The coding potential calculator tool reads FASTA data format as input. | fasta, transcript, protein coding, coding potential, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Peking University; Beijing; China |
PMID:17631615 | Free, Freely available | biotools:cpc, rid_000106 | https://bio.tools/cpc | SCR_002764 | 2026-02-14 02:00:31 | 198 | ||||||
|
rBiopaxParser Resource Report Resource Website 1+ mentions |
rBiopaxParser (RRID:SCR_002744) | software resource | A software package that provides a comprehensive set of functions for parsing, viewing and modifying BioPAX pathway data within R. At the moment BioPAX level 2 and level 3 are supported. | software package, mac os x, unix/linux, windows, data representation, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:23274212 | Free, Freely available, Available for download | biotools:rbiopaxparser, OMICS_05211 | https://github.com/frankkramer/rBiopaxParser https://bio.tools/rbiopaxparser |
SCR_002744 | rBiopaxParser - Parses BioPax files and represents them in R | 2026-02-14 02:00:19 | 4 |
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.
