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 | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
OpenEMR Resource Report Resource Website 1+ mentions |
OpenEMR (RRID:SCR_024144) | data management software, software application, software resource | Open source software for electronic health records and medical practice management solution. | electronic health records, medical practice management, | is listed by: Debian | Free, Available for download, Freely available, | https://github.com/openemr/openemr | https://sources.debian.org/src/openemr/ | SCR_024144 | SciCrunch Registry | openemr | 2026-10-24 12:49:39 | 1 | |||||||
|
Tombo Resource Report Resource Website 10+ mentions |
Tombo (RRID:SCR_024388) | data analysis software, data processing software, software application, software resource | Software suite of tools for identification of modified nucleotides from nanopore sequencing data.Used also for analysis and visualization of raw nanopore signal. | identification of modified nucleotides, nanopore sequencing data, analysis and visualization of raw nanopore signal, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/tombo/ | SCR_024388 | SciCrunch Registry | ont-tombo | 2026-10-24 12:49:40 | 18 | ||||||||
|
NW-align Resource Report Resource Website |
NW-align (RRID:SCR_024138) | alignment software, data access protocol, data processing software, image analysis software, software application, software resource, web service | Software tool as alignment program for protein sequence-to-sequence alignments based on the standard Needleman-Wunsch dynamic programming algorithm. | protein sequence-to-sequence alignments, standard Needleman-Wunsch dynamic programming algorithm, | is listed by: Debian | Free, Freely available, | https://sources.debian.org/src/nw-align/ | SCR_024138 | SciCrunch Registry | nw-align | 2026-10-24 12:49:38 | 0 | ||||||||
|
MicrobeGPS Resource Report Resource Website |
MicrobeGPS (RRID:SCR_024112) | data analysis software, data processing software, software application, software resource | Software tool for analysis of metagenomic sequencing data.Used to profile composition of metagenomic communities. Calculates quality metrics for estimated candidates and allows the user to identify false candidates. | metagenomic sequencing data analysis, profile composition of metagenomic communities, identify false candidates, | is listed by: Debian | PMID:25643362 | Free, Available for download, Freely available, | OMICS_17085 | https://sources.debian.org/src/microbegps/ | SCR_024112 | SciCrunch Registry | microbegps | 2026-10-24 12:49:39 | 0 | ||||||
|
surankco Resource Report Resource Website 1+ mentions |
surankco (RRID:SCR_024355) | simulation software, software application, software resource | Machine learning based software to score and rank contigs from de novo assemblies of next generation sequencing data. It trains with alignments of contigs with known reference genomes and predicts scores and ranking for contigs which have no related reference genome yet. | score and rank contigs, de novo assemblies of next generation sequencing data, | is listed by: Debian | PMID:26224355 | Free, Available for download, Freely available, | OMICS_09480 | https://sources.debian.org/src/surankco/ | SCR_024355 | SciCrunch Registry | 2026-10-24 12:49:40 | 1 | |||||||
|
pyscanfcs Resource Report Resource Website |
pyscanfcs (RRID:SCR_024190) | data analysis software, data processing software, software application, software resource | Software application for perpendicular line scanning fluorescence correlation spectroscopy. | perpendicular line scanning, fluorescence correlation spectroscopy, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_21694 | https://sources.debian.org/src/pyscanfcs/ | SCR_024190 | SciCrunch Registry | 2026-10-24 12:49:39 | 0 | ||||||||
|
pyranges Resource Report Resource Website 1+ mentions |
pyranges (RRID:SCR_024191) | data analysis software, data processing software, software application, software resource | Software application for efficient comparison of genomic intervals in Python. | comparison of genomic intervals, Python | is listed by: Debian | PMID:31373614 | Free, Available for download, Freely available, | https://sources.debian.org/src/python3-pyranges/ | SCR_024191 | SciCrunch Registry | 2026-10-24 12:49:39 | 7 | ||||||||
|
Chado Resource Report Resource Website 1+ mentions |
Chado (RRID:SCR_024073) | data management software, software application, software resource | Relational database schema that underlies many GMOD installations. It is capable of representing many of the general classes of data frequently encountered in modern biology such as sequence, sequence comparisons, phenotypes, genotypes, ontologies, publications, and phylogeny. It has been designed to handle complex representations of biological knowledge and should be considered one of the most sophisticated relational schemas currently available in molecular biology. The price of this capability is that the new user must spend some time becoming familiar with its fundamentals. | database schema, GMOD installations, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libchado-perl/ | SCR_024073 | SciCrunch Registry | libchado-perl | 2026-10-24 12:49:38 | 1 | ||||||||
|
yaha Resource Report Resource Website |
yaha (RRID:SCR_024365) | aligment software | Software tool as fast and flexible long read alignment with optimal breakpoint detection. | fast and flexible long-read alignment, optimal breakpoint detection, | is listed by: Debian | PMID:22829624 | Free, Available for download, Freely available, | OMICS_04675 | https://sources.debian.org/src/yaha/ | SCR_024365 | SciCrunch Registry | YAHA | 2026-10-24 12:49:40 | 0 | ||||||
|
Mustang Resource Report Resource Website 1+ mentions |
Mustang (RRID:SCR_024126) | alignment software, data processing software, image analysis software, software application, software resource | Software tool for structural alignment of multiple protein structures. Used to produce sequence alignment. Reports multiple sequence alignment and corresponding superposition of structures. | structural alignment, multiple protein structures, produce sequence alignment, | is listed by: Debian | PMID:16736488 | Free, Available for download, Freely available, | OMICS_03642 | https://sources.debian.org/src/mustang/ | SCR_024126 | SciCrunch Registry | mustang, MUltiple (protein) STructural AligNment alGorithm, MUSTANG | 2026-10-24 12:49:38 | 4 | ||||||
|
zAlign Resource Report Resource Website |
zAlign (RRID:SCR_024360) | aligment software | Software tool as local sequence aligner intended for use with large biological DNA sequences, with more than 1 Millions of base pairs. | sequence aligner, large biological DNA sequences, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_21299 | https://sources.debian.org/src/zalign/ | SCR_024360 | SciCrunch Registry | zalign | 2026-10-24 12:49:40 | 0 | |||||||
|
mlgt Resource Report Resource Website |
mlgt (RRID:SCR_001211) | mlgt | data processing software, software application, software resource | Software for processing and analysis of high throughput (Roche 454) sequences generated from multiple loci and multiple biological samples. Sequences are assigned to their locus and sample of origin, aligned and trimmed. Where possible, genotypes are called and variants mapped to known alleles. | roche, windows, os x, genotype, variant, allele, high throughput sequencing, locus, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Manchester; Manchester; United Kingdom |
THIS RESOURCE IS NO LONGER IN SERVICE | BioTools:mlgt, OMICS_02131, biotools:mlgt | https://bio.tools/mlgt, https://bio.tools/mlgt, https://bio.tools/mlgt | SCR_001211 | SciCrunch Registry | Multi-Locus Geno-Typing, mlgt: Multi-Locus Geno-Typing | 2026-10-24 12:49:47 | 0 | ||||||
|
SOAP Resource Report Resource Website 100+ mentions |
SOAP (RRID:SCR_000689) | SOAP, | data processing software, software application, software resource | Software package that provides full solution to next generation sequencing data analysis consisting of an alignment tool (SOAPaligner/soap2), a re-sequencing consensus sequence builder (SOAPsnp), an indel finder ( SOAPindel ), a structural variation scanner ( SOAPsv ), a de novo short reads assembler ( SOAPdenovo ), and a GPU-accelerated alignment tool for aligning short reads with a reference sequence. (SOAP3/GPU)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, next generation sequencing, alignment, short read, bio.tools |
lists: SOAPfusion lists: SOAPfuse lists: SOAPnuke lists: GapCloser is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: BGI; Shenzhen; China is parent organization of: SOAP3 is parent organization of: SOAPaligner/soap2 |
PMID:18227114 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154652, biotools:soap | https://bio.tools/soap | SCR_000689 | SciCrunch Registry | SOAP: short oligonucleotide alignment program, Short Oligonucleotide Analysis Package | 2026-10-24 12:49:46 | 403 | |||||
|
iDASH Resource Report Resource Website 1+ mentions |
iDASH (RRID:SCR_003524) | iDASH | data or information resource, organization portal, portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. National Center for Biomedical Computing (NCBC) that develops new algorithms, opensource tools, computational infrastructure, and services for biomedical and behavioral researchers nationwide to promote the secure sharing and consuming of biomedical and behavioral resources (software, data, and computing systems) with iDASH collaborators. The center addresses fundamental challenges to research progress by providing a secure, privacypreserving environment in which researchers can analyze genomic, transcriptomic, clinical, behavioral, and social data relevant to health. Three driving biological projects in iDASH (Molecular Phenotyping of Kawasaki Disease, Post-Marketing Surveillance of Hematologic Medications, and Individualized Intervention to Enhance Physical Activity) span the molecular-individualpopulation spectrum, and they will motivate, inform, and support tool development. iDASH will collaborate with other NCBCs and will disseminate tools via annual workshops, presentations at major conferences, and scientific publications. | data sharing, computing, biomedical, behavior, molecular, phenotyping, kawasaki disease, hematologic medication, individualized intervention, physical activity, phenotype, data set, image, cyberinfrastructure, schema, domain model, algorithm, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: DataCite is related to: National Centers for Biomedical Computing is related to: NIH Data Sharing Repositories is related to: National Centers for Biomedical Computing has parent organization: University of California at San Diego; California; USA has parent organization: University of California; California; USA |
NIH Roadmap for Bioinformatics and Computational Biology ; NHLBI U54 HL108460 |
PMID:22081224 | THIS RESOURCE IS NO LONGER IN SERVICE | https://api.datacite.org/dois?prefix=10.15147, biotools:iDASH, nif-0000-38239 | https://bio.tools/iDASH | SCR_003524 | SciCrunch Registry | iDASH Repository, Integrating Data for Analysis Anonymization and SHaring | 2026-10-24 12:49:51 | 2 | ||||
|
biobambam Resource Report Resource Website 50+ mentions |
biobambam (RRID:SCR_003308) | data processing software, software application, software resource | Software tools for read pair collation based algorithms on BAM files including * bamcollate2: reads BAM and writes BAM reordered such that alignment or collated by query name * bammarkduplicates: reads BAM and writes BAM with duplicate alignments marked using the BAM flags field * bammaskflags: reads BAM and writes BAM while masking (removing) bits from the flags column * bamrecompress: reads BAM and writes BAM with a defined compression setting. This tool is capable of multi-threading. * bamsort: reads BAM and writes BAM resorted by coordinates or query name * bamtofastq: reads BAM and writes FastQ; output can be collated or uncollated by query name | standalone software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1186/1751-0473-9-13 | Free, Available for download, Freely available | biotools:biobambam, OMICS_04664 | https://bio.tools/biobambam, https://sources.debian.org/src/biobambam2/ | SCR_003308 | SciCrunch Registry | 2026-10-24 12:49:49 | 65 | |||||||
|
Phenoscape Resource Report Resource Website 10+ mentions |
Phenoscape (RRID:SCR_003799) | Phenoscape | data or information resource, portal | Project to create a scalable infrastructure that enables linking phenotypes across different fields of biology by the semantic similarity of their descriptions. | phenotype, bio.tools |
is listed by: Debian is listed by: bio.tools is parent organization of: Teleost Anatomy Ontology is parent organization of: Vertebrate Taxonomy Ontology is parent organization of: Phenoscape Knowledgebase |
NSF DBI-1062404; NSF DBI-1062542; NSF BDI-0641025; NSF EF-0905606; NSF EF-0423641 |
biotools:Phenoscape, nlx_158096 | https://bio.tools/Phenoscape | SCR_003799 | SciCrunch Registry | 2026-10-24 12:49:49 | 10 | |||||||
|
FASTX-Toolkit Resource Report Resource Website 1000+ mentions |
FASTX-Toolkit (RRID:SCR_005534) | data processing software, software application, software resource, software toolkit | Software tool as collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. | Short reads, FASTA file, FASTQ file, preprocessing, command line tools, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Cold Spring Harbor Laboratory |
SCR_019035, SCR_015042, biotools:fastx-toolkit, OMICS_01045 | https://github.com/agordon/fastx_toolkit, https://bio.tools/fastx-toolkit | SCR_005534 | SciCrunch Registry | FASTQ/A short-reads pre-processing tools | 2026-10-24 12:49:51 | 2864 | ||||||||
|
Mammalian Gene Collection Resource Report Resource Website 10+ mentions |
Mammalian Gene Collection (RRID:SCR_007024) | MGC | biomaterial supply resource, cell repository, material resource | NIH initiative project to provide full-length open reading frame (FL-ORF) clones for human, mouse, and rat genes, cow. MGC cDNA clones were obtained by screening of cDNA libraries, by transcript-specific RT-PCR cloning, and by DNA synthesis of cDNA inserts. All MGC sequences are deposited in GenBank and clones can be purchased from distributors of IMAGE consortium. With conclusion of MGC project in March 2009, GenBank records of MGC sequences will be frozen, without further updates. Since definition of what constitutes full-length coding region for some of genes and transcripts for which they have MGC clones will likely change in future, users planning to order MGC clones will need to monitor for these changes. Users can make use of genome browsers and gene-specific databases, such as the UCSC Genome browser, NCBI's Map Viewer, and Entrez Gene, to view relevant regions of genome (browsers) or gene-related information (Entrez Gene). | cell line, cdna, frozen, clone, vector, gene, open reading frame, sequence, expressed sequence tag, bio.tools, FASEB list |
is listed by: One Mind Biospecimen Bank Listing is listed by: bio.tools is listed by: Debian is related to: One Mind Biospecimen Bank Listing is related to: NIDDK Information Network (dkNET) is related to: ATCC is related to: GenBank is related to: Invitrogen Clones is related to: Open Biosystems is related to: Zebrafish Gene Collection has parent organization: National Cancer Institute |
NIH Blueprint for Neuroscience Research | Free, Freely available | biotools:mammalian_gene_collection, nif-0000-00195 | https://bio.tools/mammalian_gene_collection | SCR_007024 | SciCrunch Registry | Mammalian Gene Collection | 2026-10-24 12:49:54 | 46 | |||||
|
Sickle Resource Report Resource Website 1000+ mentions |
Sickle (RRID:SCR_006800) | Sickle | data processing software, software application, software resource | Software tool for windowed adaptive trimming for fastq files using quality. Supports quality values like Illumina, Solexa, and Sanger. Takes the quality values and slides a window across them whose length is 0.1 times the length of the read. | bio.tools, windowed, adaptive, trimming, FASTQ, quality, value, read |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | OMICS_01077, biotools:sickle, SCR_016901 | https://bio.tools/sickle, https://sources.debian.org/src/sickle/ | SCR_006800 | SciCrunch Registry | sickle - A windowed adaptive trimming tool for FASTQ files using quality | 2026-10-24 12:49:53 | 1664 | ||||||
|
SeqTrace Resource Report Resource Website 50+ mentions |
SeqTrace (RRID:SCR_005580) | SeqTrace | data processing software, software application, software resource | A software application for viewing and processing DNA sequencing chromatograms (trace files) that makes it easy to quickly generate high-quality finished sequences from a large number of trace files. SeqTrace can automatically identify, align, and compute consensus sequences from matching forward and reverse traces, filter low-quality base calls, and perform end trimming of finished sequences. The finished DNA sequences can then be exported to common sequence file formats, such as FASTA. SeqTrace also includes a full-featured trace file viewer and editor. You can view your sequencing chromatograms at a variety of scales and zoom levels, simultaneously view matching forward and reverse traces, edit the called bases, and export individual DNA sequences as well as forward/reverse alignments. SeqTrace supports popular trace file formats, including ABIF, SCF, and ZTR. | dna sequencing trace file, dna sequencing, trace file, trace, python, gtk, chromatogram, graphic, sequence analysis, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code has parent organization: University of Colorado Boulder; Colorado; USA |
PMID:22942788 | GNU General Public License, v3 | OMICS_01021, biotools:seqtrace | https://bio.tools/seqtrace | SCR_005580 | SciCrunch Registry | Seqtrace - User-friendly software for viewing and processing DNA sequencing trace files | 2026-10-24 12:49:52 | 64 |
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.
