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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
PAZAR Resource Report Resource Website 10+ mentions |
PAZAR (RRID:SCR_005410) | PAZAR | data repository, storage service resource, data or information resource, service resource, software resource, database | Database that unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. The flexible PAZAR schema permits the representation of diverse information derived from experiments ranging from biochemical protein-DNA binding to cellular reporter gene assays. Data collections can be made available to the public, or restricted to specific system users. The data ''boutiques'' within the shopping-mall-inspired system facilitate the analysis of genomics data and the creation of predictive models of gene regulation., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | transcription factor, target gene, regulatory sequence, transcription factor profile, annotation, sequence, profile, transcription factor binding profile, chip, chip-seq, gene, cis-regulatory element, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of British Columbia; British Columbia; Canada has parent organization: SourceForge |
PMID:18971253 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00540, biotools:pazar | https://bio.tools/pazar | SCR_005410 | 2026-02-14 02:01:06 | 32 | ||||||
|
Maq Resource Report Resource Website 50+ mentions |
Maq (RRID:SCR_005485) | Maq | software resource | A set of programs that map and assemble fixed-length Solexa/SOLiD reads in a fast and accurate way. | command-line, curses/ncurses, opengl, c, c++, perl, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: SourceForge |
DOI:10.1101/gr.078212.108 | GNU General Public License, v2 | biotools:maq, OMICS_00668 | https://bio.tools/maq https://sources.debian.org/src/maq/ |
SCR_005485 | mapass2, Mapping and Assembly with Quality, Mapping and Assembly with Qualities, Maq: Mapping and Assembly with Qualities | 2026-02-14 02:00:56 | 69 | |||||
|
MACE Resource Report Resource Website 1000+ mentions |
MACE (RRID:SCR_005520) | MACE | software resource | A bioinformatics tool dedicated to analyze ChIP-exo data: 1) Sequencing depth normalization and nucleotide composition bias correction. 2) Signal consolidation and noise reduction. 3) Single base resolution border detection. 4) Border matching. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00520 | SCR_005520 | MACE: Model based Analysis of ChIP-exo | 2026-02-14 02:01:07 | 1172 | |||||||||
|
TreQ Resource Report Resource Website |
TreQ (RRID:SCR_005505) | TreQ | software resource | A software read mapper for high-throughput DNA sequencing reads, in particular one to several hundred nucleotides in length, and for large edit distance between sequencing read and match in the reference genome. It can cope particularly well with indels for single-best hit recall of 200nt reads simulated from the human reference genome. TreQ performs best at a running time comparable to BWA at large edit distance settings. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: Rutgers University; New Jersey; USA |
PMID:22962448 | GNU General Public License | OMICS_00695, biotools:treq | https://bio.tools/treq | SCR_005505 | TreQ: Indel-tolerant Read Mapper | 2026-02-14 02:00:56 | 0 | |||||
|
netClass Resource Report Resource Website |
netClass (RRID:SCR_005672) | netClass | software resource | An R package for network-based feature (gene) selection for biomarkers discovery via integrating biological information. The package adapts the following 5 algorithms for classifying and predicting gene expression data using prior knowledge: # average gene expression of pathway (aep); # pathway activities classification (PAC); # Hub network classification (hubc); # filter via top ranked genes (FrSVM); # network smoothed t-statistic (stSVM). | protein-protein interaction network, biomarker discovery, classification, micoarray, gene expression profile, protein-protein interaction, gene expression, gene, biomarker |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24443376 | Free, Public | OMICS_02241 | SCR_005672 | 2026-02-14 02:00:57 | 0 | |||||||
|
go-moose Resource Report Resource Website |
go-moose (RRID:SCR_005666) | go-moose | data analysis software, software resource, data processing software, software application | go-moose is intended as a replacement for the aging go-perl and go-db-perl Perl libraries. It is written using the object oriented Moose libraries. It can be used for performing a number of analyses on GO data, including the remapping of GO annotations to a selected subset of GO terms. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | software library, slimmer-type tool, analysis, gene ontology, other analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: go-perl is related to: go-db-perl has parent organization: SourceForge has parent organization: Berkeley Bioinformatics Open-Source Projects has parent organization: Lawrence Berkeley National Laboratory |
Free for academic use | nlx_149189 | SCR_005666 | 2026-02-14 02:01:08 | 0 | ||||||||
|
TMAJ Resource Report Resource Website 10+ mentions |
TMAJ (RRID:SCR_005601) | TMAJ | software resource | Open-source software to support information and images related to tissue micro-arrays. It contains support for multiple organ systems, multiple users, image analysis, and is designed to be compliant with HIPPA regulations. Patients, specimens, blocks, slides, cores, images, and scores can all be stored and viewed. Features include advanced security, custom dynamic fields, and an image analysis program. | tissue microarray, java, java swing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Johns Hopkins University; Maryland; USA has parent organization: SourceForge |
GNU General Public License, v3 | biotools:tmaj, OMICS_00823 | https://bio.tools/tmaj | SCR_005601 | TMAJ Software Project | 2026-02-14 02:00:56 | 10 | ||||||
|
Maqview Resource Report Resource Website |
Maqview (RRID:SCR_005632) | MaqView | data visualization software, software resource, data processing software, software application | A graphical read alignment viewer specifically designed for the Maq alignment file and allows you to see the mismatches, base qualities and mapping qualities. It is highly efficient in speed, memory and disk usage. Maqview is based on OpenGL and is known to work on both Mac OS X and Linux. Porting to Windows is in principle easy. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
DOI:10.1101/gr.078212.108 | GNU General Public License | OMICS_00889, biotools:maqview | https://bio.tools/maqview https://sources.debian.org/src/maqview/ |
SCR_005632 | Mapping and Assembly with Qualities Viewer, M.A.Q Viewer | 2026-02-14 02:00:56 | 0 | |||||
|
Staden Package Resource Report Resource Website 50+ mentions |
Staden Package (RRID:SCR_005629) | software resource | A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows. | c, unix/linux, sequence assembly, dna/protein analysis, spin, sequence alignment, genome, genome viewer, c++, fortran, tcl, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:20513662 DOI:10.1093/bioinformatics/btq268 |
BSD License | OMICS_00894, biotools:staden | https://bio.tools/staden https://sources.debian.org/src/staden/ |
SCR_005629 | Staden Package | 2026-02-14 02:01:09 | 79 | ||||||
|
Mindtouch DekiWiki Resource Report Resource Website 1+ mentions |
Mindtouch DekiWiki (RRID:SCR_003425) | MindTouch | software resource, source code, commercial organization | A web based social authoring and publishing environment that adheres to open standards and RESTful design principals. It provides wiki-like ease of use with a sophisticated web services framework for rapid application development, creating flexible workflows and rapid integration. MindTouch creates a vibrant real-time information fabric by federating content from across enterprise silos, such as CRM, ERP, file servers, email, databases, web services and more. | authoring, publishing, standard, web service, cloud |
is listed by: FORCE11 is listed by: Biositemaps has parent organization: University of Wisconsin-Madison; Wisconsin; USA has parent organization: SourceForge |
Free, Freely available | nif-0000-33097 | http://sourceforge.net/projects/dekiwiki/ https://www.force11.org/node/4733 |
SCR_003425 | MindTouch Core, DekiWiki, MindTouch Deki Wiki, Deki Wiki, MindTouch (frmly deki wiki) | 2026-02-14 02:00:33 | 2 | ||||||
|
MIAPA Resource Report Resource Website 1+ mentions |
MIAPA (RRID:SCR_003777) | MIAPA | data or information resource, narrative resource, standard specification | Central hub for resources related to developing and deploying a Minimal Information for a Phylogenetic Analysis (MIAPA) standard. | phylogeny, dna, amino acid sequence |
is listed by: Minimum Information for Biological and Biomedical Investigations is listed by: GitHub is listed by: SourceForge |
PMID:16901231 | nlx_158100 | https://github.com/miapa/miapa/blob/master/checklist/MIAPA-checklist.md http://mibbi.sourceforge.net/projects/MIAPA.shtml |
SCR_003777 | Minimal Information for a Phylogenetic Analysis | 2026-02-14 02:00:36 | 1 | ||||||
|
SeqExpress Resource Report Resource Website |
SeqExpress (RRID:SCR_004013) | software resource | A cross-platform software that estimates gene/isoform expression level via mRNA-Seq data. SeqExpress exams the Sequencing bias in mRNA-Seq and correct it to get more accurate estimation. | c++, mrna-seq, qt |
is listed by: OMICtools has parent organization: SourceForge |
PMID:15746290 PMID:14988116 |
GNU General Public License v2 | OMICS_01289 | SCR_004013 | 2026-02-14 02:00:35 | 0 | ||||||||
|
Drosophila anatomy and development ontologies Resource Report Resource Website |
Drosophila anatomy and development ontologies (RRID:SCR_001607) | FBbt | data or information resource, ontology, controlled vocabulary | A structured controlled vocabulary of the anatomy of Drosophila melanogaster. These ontologies are query-able reference sources for information on Drosophila anatomy and developmental stages. They also provide controlled vocabularies for use in annotation and classification of data related to Drosophila anatomy, such as gene expression, phenotype and images. They were originally developed by FlyBase, who continue to maintain them and have used them for over 200,000 annotations of phenotypes and expression. Extensive use of synonyms means that, given a suitably sophisticated autocomplete, users can find relevant content by searching with almost any anatomical term they find in the literature. These ontologies are developed in the web ontology language OWL2. Their extensive formalization in OWL can be used to drive sophisticated query systems. | anatomy, development, developmental stage, gene expression, phenotype, owl |
is related to: OBO is related to: Flannotator is related to: REDfly Regulatory Element Database for Drosophilia is related to: Bgee: dataBase for Gene Expression Evolution has parent organization: FlyBase has parent organization: SourceForge |
NHGRI P41 HG000739 | Free, Freely available | nlx_153871 | SCR_001607 | Drosophila anatomy & dev ontologies | 2026-02-14 02:00:13 | 0 | ||||||
|
BACContigEditor Resource Report Resource Website |
BACContigEditor (RRID:SCR_001617) | BACContigEditor | software resource | A simple sequence alignment editing tool, written in Java. | matlab |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_00875 | SCR_001617 | 2026-02-14 02:00:04 | 0 | ||||||||
|
DNACLUST Resource Report Resource Website 1+ mentions |
DNACLUST (RRID:SCR_001771) | software resource | Software program for clustering large number of short similar DNA sequences. It was originally designed for clustering targeted 16S rRNA pyrosequencing reads. | cluster, dna sequence, gene, 16s rrna pyrosequencing read, microbiome |
is listed by: OMICtools is listed by: Human Microbiome Project is listed by: Debian has parent organization: SourceForge |
PMID:21718538 DOI:10.1186/1471-2105-12-271 |
Free, Available for download, Freely available | OMICS_01955 | https://sources.debian.org/src/dnaclust/ | SCR_001771 | DNAClust | 2026-02-14 02:00:10 | 9 | ||||||
|
BMDExpress Resource Report Resource Website 10+ mentions |
BMDExpress (RRID:SCR_006823) | BMDExpress | data analysis software, software resource, data processing software, software application | Bioinformatics tool used to analyze microarray dose-response data. The analysis provides benchmark dose estimates at which different cellular processes are altered in toxicogenomic experiments. | bioinformatics, microarray, software, toxicogenomics |
is related to: The Hamner Institute for Health Sciences: BMDExpress and The multiple-path particle dosimetry has parent organization: SourceForge |
MIT License | nlx_152743 | SCR_006823 | 2026-02-14 02:01:24 | 32 | ||||||||
|
mubiomics Resource Report Resource Website 1+ mentions |
mubiomics (RRID:SCR_006785) | mubiomics | software resource | A set of scripts (mostly python) for processing reads generated by the Roche 454 or Illumina next-gen sequencing platforms. Included are quality control, read demultiplexing and microbiome characterisation scripts for use with usearch, pplacer and RDP classifier. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01059 | SCR_006785 | mubiomics - Scripts for processing next-gen sequencing data | 2026-02-14 02:01:15 | 3 | |||||||||
|
Qudaich Resource Report Resource Website |
Qudaich (RRID:SCR_006775) | Qudaich | software resource | A software package for local sequence alignment for next-generation sequencing (NGS) data. It generates the pairwise local alignments between a query dataset against a database. The main design purpose of qudaich is to focus on datasets from next generation sequencing. These the datasets generally have hundreds of thousand sequences or more, and so, the input database should contain large number of sequences. Qudaich is flexible and its algorithmic structure imposes no restriction on the absolute limit of the acceptable read length, but the current version of qudaich allow read length <2000 bp. Qudaich can be used to align DNA, translated DNA and protein sequences. | next-generation sequencing, alignment |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00678 | SCR_006775 | Queries and unique database alignment inferred by clustering homologs | 2026-02-14 02:01:22 | 0 | ||||||||
|
Adverse Event Ontology Resource Report Resource Website |
Adverse Event Ontology (RRID:SCR_006807) | AEO | data or information resource, ontology, controlled vocabulary | AEO represents the Adverse Event Ontology, a community-driven ontology developed to standardize and integrate data on biomedical adverse events (e.g., vaccine adverse events) and support computer-assisted reasoning. The AEO also can be found in BioPortal, http://bioportal.bioontology.org/ontologies/45534?p=terms | has parent organization: SourceForge | nlx_44108 | SCR_006807 | 2026-02-14 02:01:22 | 0 | ||||||||||
|
GBS barcode splitter Resource Report Resource Website |
GBS barcode splitter (RRID:SCR_006799) | GBS barcode splitter | software resource | PERL script used to split barcode of Illumina sequencing data created by GBS protocol (www.maizegenetics.net). The barcode has variable size. Paired-end reads are supported. | illumina |
is listed by: OMICtools has parent organization: SourceForge |
Free | OMICS_01050 | SCR_006799 | GBS barcode splitter - PERL script for split GBS reads by barcode | 2026-02-14 02:01:22 | 0 |
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