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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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
redcap-importer Resource Report Resource Website |
redcap-importer (RRID:SCR_016032) | data acquisition software, software application, data processing software, software resource | Software that automates the process of retrieving and converting data to the format of a RedCap table and allows selection of directories and files for import. | automate, process, retrvinig, converting, data, format, research, electronic, data, capture, table, selection, directory, import | is related to: University of California at San Diego; California; USA | NIDA U24 DA041123 | Free, Available for download | SCR_016032 | 2026-02-16 09:48:56 | 0 | |||||||||
|
NeMOarchive Resource Report Resource Website 100+ mentions |
NeMOarchive (RRID:SCR_016152) | NeMO | data repository, database, service resource, storage service resource, data or information resource | Data repository specifically focused on storage and dissemination of omic data generated from BRAIN Initiative and related brain research projects. Data repository and archive for BCDC and BICCN project, among others. NeMO data include genomic regions associated with brain abnormalities and disease, transcription factor binding sites and other regulatory elements, transcription activity, levels of cytosine modification, histone modification profiles and chromatin accessibility. | omic, neuroscience, neurobiology, bcbc, biccn, nih, brain, genomic, region, abnormal, transcription, factor, binding, site, chromatin, regulatory, element, data |
is used by: BRAIN Initiative Cell Atlas Network is used by: BICCN is recommended by: BRAIN Initiative is related to: NeMO Analytics has parent organization: University of Maryland School of Medicine; Maryland; USA |
NIMH MH114788; BRAIN Initiative |
Free, Freely available | https://data.nemoarchive.org/ | SCR_016152 | NeMO Archive, Neuroscience Multi-omic Data Archive, The Neuroscience Multi-Omic Archive, Neuroscience Multi-Omic Archive | 2026-02-16 09:48:59 | 113 | ||||||
|
Bio-tradis Resource Report Resource Website 50+ mentions |
Bio-tradis (RRID:SCR_015993) | TraDIS:Transposon Directed Insertion Sequencing | software application, data processing software, software toolkit, sequence analysis software, data analysis software, software resource | Analysis software for the output from TraDIS (Transposon Directed Insertion Sequencing) analyses of dense transposon mutant libraries. The Bio-Tradis analysis pipeline is implemented as an extensible Perl library which can either be used as is, or as a basis for the development of more advanced analysis tools. | software, tool, analysis, data, sequencing, insertion, transponson, direct, mutant, library, perl, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust WT098051; Alexander von Humboldt Stiftung/Foundation ; Medical Research Council G1100100/1 |
PMID:26794317 DOI:10.1093/bioinformatics/btw022 |
Free, Available for download, Freely available | OMICS_11083, biotools:bio-tradis | https://bio.tools/bio-tradis https://sources.debian.org/src/bio-tradis/ |
SCR_015993 | 2026-02-16 09:48:55 | 51 | |||||
|
HyPhy Resource Report Resource Website 1000+ mentions |
HyPhy (RRID:SCR_016162) | software application, data processing software, software toolkit, sequence analysis software, data analysis software, software resource | Open source software package for comparative sequence analysis using stochastic evolutionary models. Used for analysis of genetic sequence data in particular the inference of natural selection using techniques in phylogenetics, molecular evolution, and machine learning. | analysis, genetic, sequence, multiply, alignment, rate, pattern, data, evolution, platform, python, r, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
NSF DBI-0096033; NSF DEB-9996118; NIH R01 AI47745; NIH U01 AI43638; University of California Universitywide AIDS Research Program IS02-SD-701; University of California ; San Diego Center for AIDS Research/NIAID Developmental Award 2 P30 AI36214; NIGMS R01 |
PMID:15509596 | Free, Available for download, Freely available | SCR_016271, biotools:HyPhy, OMICS_04235 | https://sources.debian.org/src/hyphy-pt/ https://veg.github.io/hyphy-site/ https://github.com/veg/hyphy https://bio.tools/HyPhy |
SCR_016162 | HyPhy:Hypothesis Testing using Phylogenies, Hyphy-pt | 2026-02-16 09:48:58 | 1497 | |||||
|
Indelible Resource Report Resource Website 10+ mentions |
Indelible (RRID:SCR_016163) | software application, software resource, simulation software | Software that generates nucleotide, amino acid and codon sequence data by simulating insertions and deletions (indels) as well as substitutions. It is used for biological sequence simulation of multi-partitioned nucleotide, amino-acid, or codon data sets through the processes of insertion, deletion, and substitution in continuous time. | indel, insertion, deletion, biological, sequence, simulation, multi-partitioned, nucleotide, amio-acid, codon, data, set, insertion, deletion, substitution, continous, time, non-homogeneous, non-stationary, phylogeny, simulator, evolution |
is listed by: Debian is listed by: OMICtools |
EPSRC/MRC Doctoral Training Centre studentship ; BBSRC |
PMID:19423664 | Free, Available for download | OMICS_15369 | https://sources.debian.org/src/indelible/ | SCR_016163 | 2026-02-16 09:48:58 | 23 | ||||||
|
FIONASITE Resource Report Resource Website |
FIONASITE (RRID:SCR_016012) | software application, data processing software, data management software, software resource, data transfer software, data acquisition software | Software for uploading data to FIONA and capturing MR images and k-space data from medical image systems. It provides a web-interface to automate the data review (image viewer), integrate with the centralized electronic data record for assigning anonymized id's, and forward the data to the central archive. | automate, data, upload, collection, network, appliance, abcd, study | is related to: University of California at San Diego; California; USA | NIDA U24 DA041123 | Free, Available for download | SCR_016014, SCR_016013 | http://qi.ucsd.edu/news-article.php?id=2342&go=newer | SCR_016012 | 2026-02-16 09:48:56 | 0 | |||||||
|
Minimally-Processed-Image-Sharing Resource Report Resource Website |
Minimally-Processed-Image-Sharing (RRID:SCR_016016) | software application, data processing software, data distribution software, data management software, software resource, data transfer software | Software to share ABCD minimally processed data. It uploads minimally-processed MRI data to the NDA ( Non-Disclosure Agreement) ABCD (Adolescent Brain Cognitive Development) repository. | share, data, minimally processed, image, files, fast-track, non-processed, link, store, upload |
is related to: University of California at San Diego; California; USA works with: ABCD Study |
NIDA U24 DA041123 | SCR_016016 | 2026-02-16 09:48:56 | 0 | ||||||||||
|
Microsoft Excel Resource Report Resource Website 10000+ mentions |
Microsoft Excel (RRID:SCR_016137) | software application, data processing software, data visualization software, data analysis software, software resource | Software application with data analysis tools and spreadsheet templates to track and visualize data. It is used to manage and process data. | data, process, manage, analyze, spreadsheet, template, track, visualize, graph |
is related to: XLSTAT is related to: Statcel3 has plug in: OVAL has plug in: easyGV |
Microsoft | Commercially available, Trial available | SCR_016137 | , MS Excel | 2026-02-16 09:48:59 | 81724 | ||||||||
|
Fast-Track-Image-Sharing Resource Report Resource Website |
Fast-Track-Image-Sharing (RRID:SCR_016021) | software application, data processing software, data management software, software resource, data transfer software | Software for sharing the ABCD (Adolescent Brain Cognitive Development) study data on the National Data Archive (NDA). | sharing, tool, study, data, national, archive, abcd, nda, adolescent | is related to: University of California at San Diego; California; USA | NIDA U24 DA041123 | Free, Available for download | SCR_016021 | 2026-02-16 09:48:58 | 0 | |||||||||
|
eprime-data-clean Resource Report Resource Website |
eprime-data-clean (RRID:SCR_016020) | data processing software, software application, software resource, data management software | Software to convert E-Prime (software tool for psychology computerized experiment design, data collection, and analysis) generated files to CSV files without errors during conversion. The ABCD project is using E-Prime to run behavioral tests. | convert, data, psychology, computerized, experiment, design, collection, analysis, generate, file, errors, conversion, abcd |
is related to: University of California at San Diego; California; USA works with: ABCD Study |
NIDA U24 DA041123 | Free, Available for download | SCR_016020 | 2026-02-16 09:48:56 | 0 | |||||||||
|
geocoding Resource Report Resource Website 10+ mentions |
geocoding (RRID:SCR_016007) | software application, data processing software, data analytics software, data analysis software, software resource | Software that uses a geo-location database to determine individuals' residential environment in Adolescent Brain Cognitive Development (ABCD) study. It performs queries given individuals' residential history in longitude and latitude. | software, data, analysis, geo-location, residential, environment, abcd, study |
has parent organization: University of California at San Diego; California; USA works with: ABCD Study |
NIDA U24 DA041123 | Free, Available for download | SCR_016007 | ABCD geocoding, ABCD geocoding project, geocoding project | 2026-02-16 09:48:55 | 23 | ||||||||
|
Gentle Resource Report Resource Website 1+ mentions |
Gentle (RRID:SCR_016127) | software application, data processing software, software toolkit, sequence analysis software, data analysis software, software resource | Software for DNA and amino acid editing, database management, plasmid maps, It can also be used for restriction and ligation, alignments, sequencer data import, calculators, gel image display, PCR, and more. | editing, database, management, plasmid maps, restriction, ligation, alignments, sequence, data, import, calculator, gel, image, display, PCR, cloning, genetic |
is listed by: Debian is listed by: OMICtools has parent organization: University of Cologne; Cologne; Germany |
Free Software Foundation | Free, Available for download | OMICS_18307 | https://sources.debian.org/src/gentle/ | SCR_016127 | GENtle | 2026-02-16 09:48:57 | 6 | ||||||
|
Bio++ Resource Report Resource Website 50+ mentions |
Bio++ (RRID:SCR_016055) | software development tool, software application, software toolkit, software library, software resource | Software providing a set of ready-to-use C++ libraries as re-usable tools to visualize, edit, print and output data for bioinformatics. It uses sequence analysis, phylogenetics, molecular evolution and population genetics to help to write programs., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | phylogenetic, molecular evolution, genetic, program, write, tool, visualize, edit, print, data, bioinformatic, sequence analysis, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_15696, biotools:biopp | https://sources.debian.org/src/bppsuite/ https://groups.google.com/forum/#!categories/biopp-help-forum/all-questions https://github.com/BioPP https://bio.tools/biopp |
SCR_016055 | Bppsuite, Bppphyview, Bio++ program suite, Bio++ Phylogenetic Viewer | 2026-02-16 09:48:56 | 65 | |||||||
|
Dazzler Resource Report Resource Website 10+ mentions |
Dazzler (RRID:SCR_016069) | software application, software toolkit, data management software, software library, database, software resource, data or information resource | Software library and database to manage nucleotide sequencing read data. It stores the source Pacbio read information in such a way that it can re-create the original input data, thus permitting a user to remove the (effectively redundant) source files and avoid duplicating data. | manage, nucleotide, sequencing, data, database, library, storage, pacbio, read |
is used by: Daligner is listed by: Debian is related to: Max Planck Institute for Molecular Genetics; Berlin; Germany |
Free, Available for download | https://sources.debian.org/src/dazzdb/ https://dazzlerblog.wordpress.com/command-guides/dazz_db-command-guide/ |
SCR_016069 | Dazzdb, DAZZ_DB, The Dazzler Database | 2026-02-16 09:48:56 | 14 | ||||||||
|
Lifebit Deploit Resource Report Resource Website 1+ mentions |
Lifebit Deploit (RRID:SCR_016428) | software application, data analysis service, analysis service resource, data management software, software resource, production service resource, service resource | Platform for computing management for data analysis on the cloud from the Lifebit company. Allows the computational analyses to be permanently linked to live analyses pipelines. | Lifebit, compute, management, data, analysis, cloud, integrate, data, reproduce, transparent, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:28398311 | Commercially available | biotools:nextflow | https://bio.tools/nextflow | SCR_016428 | 2026-02-16 09:49:01 | 2 | |||||||
|
Ximmer Resource Report Resource Website 1+ mentions |
Ximmer (RRID:SCR_016427) | software application, data processing software, data visualization software, data analysis software, software resource, simulation software | Software to help users of targeted high throughput genomic sequencing data to accurately detect copy number variants (CNVs). Framework for running and evaluating other copy number detection tools.Used for evaluating and improving performance of CNV detection in exome and targeted sequencing data. | cnv, copy, number, variant, exome, targeted, sequencing, data, next, generation, genomic | is listed by: OMICtools | National Human Genome Research Institute ; National Eye Institute ; National Heart Lung and Blood Institute ; Australian National Health and Medical Research Council ; Victorian State Government |
DOI:10.1101/260927 | Open source, Free, Available for download, Freely available | https://omictools.com/ximmer-tool http://ximmer.org |
SCR_016427 | 2026-02-16 09:49:01 | 4 | |||||||
|
GOTrack Resource Report Resource Website 1+ mentions |
GOTrack (RRID:SCR_016399) | web service, data access protocol, database, software resource, data or information resource | Open source web-based system and database that provides access to historical records and trends in the Gene Ontology (GO) and GO annotations (GOA). Used for monitoring changes in the Gene Ontology and their impact on genomic data analysis. | database, system, access, historical, monitor, record, gene, genomic, data, analysis, ontology, annotation, bioinformatics |
is listed by: OMICtools is related to: University of British Columbia; British Columbia; Canada |
NIH MH111099; NSERC Discovery Grant ; Canadian Foundation for Innovation infrastructure ; CIHR |
DOI:10.1101/320861 | Free, Available for download, Freely available | https://github.com/PavlidisLab/gotrack https://omictools.com/gotrack-tool |
SCR_016399 | 2026-02-16 09:49:01 | 1 | |||||||
|
Archive of Data on Disability to Enable Policy (ADDEP) Resource Report Resource Website |
Archive of Data on Disability to Enable Policy (ADDEP) (RRID:SCR_016315) | ADDEP | service resource, data repository, data or information resource, storage service resource | Provides access to data including wide range of topics related to disability. ADDEP data can be used to better understand and inform the implementation of Americans with Disabilities Act and other disability policies. | Data, access, disability | is recommended by: National Library of Medicine | NICHD ; NINDS ; NIBIB |
SCR_016315 | Archive of Data on Disability to Enable Policy | 2026-02-16 09:49:00 | 0 | ||||||||
|
Suite2P Resource Report Resource Website 50+ mentions |
Suite2P (RRID:SCR_016434) | software application, data processing software, software toolkit, data analysis software, image processing software, software resource | Software package for processing two-photon recordings. Available together with a graphical user interface that allows manual curation of the results. Used in two-photon microscopy for the analysis of data from two-photon imaging. Registers raw movies, detects active cells, extracts their calcium traces and infers their spike times. | two, photon, microscopy, processing, image, data, record |
is related to: MATLAB has parent organization: University College London; London; United Kingdom |
Free, Available for download, Freely available | SCR_016434 | 2026-02-16 09:49:01 | 71 | ||||||||||
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OmicsBean Resource Report Resource Website 100+ mentions |
OmicsBean (RRID:SCR_016322) | software application, data processing software, data analytics software, data analysis software, software resource | Software tool for multi-omics data analysis that can perform complex and personalized analysis. Network regulation and molecular mechanism models can be customized according to the requirements of the users. | GeneForHealth Biotech Inc (GFK), data, analysis, genome, proteome, metabolome, network, molecular, mechanism, model, collect, store, analytic, multi, omic | Commercially available, Demo available | SCR_016322 | 2026-02-16 09:49:00 | 145 |
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