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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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FIONASITE Resource Report Resource Website |
FIONASITE (RRID:SCR_016012) | data management software, software application, data transfer software, data processing software, data acquisition software, software resource | 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 | 2026-02-17 10:02:38 | 0 | |||||||
|
Minimally-Processed-Image-Sharing Resource Report Resource Website |
Minimally-Processed-Image-Sharing (RRID:SCR_016016) | data management software, software application, data transfer software, data processing software, data distribution software, software resource | 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 | 2026-02-17 10:02:56 | 0 | ||||||||||
|
Fast-Track-Image-Sharing Resource Report Resource Website |
Fast-Track-Image-Sharing (RRID:SCR_016021) | data management software, software application, data transfer software, data processing software, software resource | 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 | 2026-02-17 10:03:21 | 0 | |||||||||
|
eprime-data-clean Resource Report Resource Website |
eprime-data-clean (RRID:SCR_016020) | data management software, software application, data processing software, software resource | 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 | 2026-02-17 10:02:57 | 0 | |||||||||
|
Gentle Resource Report Resource Website 1+ mentions |
Gentle (RRID:SCR_016127) | software application, data processing software, data analysis software, sequence analysis software, software resource, software toolkit | 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 | 2026-02-17 10:03:21 | 6 | ||||||
|
Bio++ Resource Report Resource Website 50+ mentions |
Bio++ (RRID:SCR_016055) | software development tool, software application, software resource, software toolkit, software library | 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 | 2026-02-17 10:02:38 | 65 | |||||||
|
Dazzler Resource Report Resource Website 10+ mentions |
Dazzler (RRID:SCR_016069) | data management software, software application, data or information resource, database, software resource, software toolkit, software library | 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 | 2026-02-17 10:03:21 | 14 | ||||||||
|
DEAP - Data Exploration and Analysis Portal Resource Report Resource Website 10+ mentions |
DEAP - Data Exploration and Analysis Portal (RRID:SCR_016158) | DEAP | data access protocol, web service, software resource | Web service for data exploration and analysis of the ABCD Study - the largest long-term study of brain development and child health in the United States. | data, exploration, analysis, portal, brain, development, child, health, United, States, long, term, study | is related to: ABCD Study | Free, Available for download | SCR_016158 | DEAP: Data Exploration and Analysis Portal | 2026-02-17 10:02:58 | 18 | ||||||||
|
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 | data or information resource, service resource, data repository, 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 | 2026-02-17 10:03:00 | 0 | ||||||||
|
NeMOarchive Resource Report Resource Website 100+ mentions |
NeMOarchive (RRID:SCR_016152) | NeMO | storage service resource, data or information resource, database, service resource, data repository | 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 | 2026-02-17 10:03:19 | 113 | ||||||
|
ANNOgesic Resource Report Resource Website 10+ mentions |
ANNOgesic (RRID:SCR_016326) | software application, standalone software, data processing software, data analysis software, software resource, software toolkit | Software tool for bacterial/archaeal RNA-Seq based genome annotations. Used for integrating, detecting, predicting, and grouping RNA-Seq data. | bacterial, archaeal, RNA, sequencing, data, analysis, genome, annotation, statistic, visualization, protein, interaction, prediction, grouping, go, ontology, gene, differential, circular |
is related to: Infernal is related to: Vienna RNA is related to: Biopython is related to: MEME Suite - Motif-based sequence analysis tools is related to: Segemehl |
Free, Freely available, Available for download | SCR_016326 | 2026-02-17 10:03:00 | 10 | ||||||||||
|
HyPhy Resource Report Resource Website 1000+ mentions |
HyPhy (RRID:SCR_016162) | software application, data processing software, data analysis software, sequence analysis software, software resource, software toolkit | 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 | 2026-02-17 10:02:39 | 1497 | |||||
|
Microsoft Excel Resource Report Resource Website 10000+ mentions |
Microsoft Excel (RRID:SCR_016137) | software application, data processing software, data analysis software, software resource, data visualization software | 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 | 2026-02-17 10:03:22 | 81724 | ||||||||
|
CycIF.org Resource Report Resource Website 10+ mentions |
CycIF.org (RRID:SCR_016267) | CycIF.org | narrative resource, data or information resource, immunofluorescence, web page, immuno detection protocol, experimental protocol | Web page for cyclic immunofluorescence. It lists several downloadable data and software pertaining to cyclic immunofluorescence. | immunofluorescence, cyclic, cycif, data, software, single cell, numeric, dataset, intratumoural, heterogeneity | has parent organization: LINCS Data Portal | NHLBI U54 HL127365 | PMID:26399630 | Public | SCR_016267 | cycif.org | 2026-02-17 10:03:23 | 13 | ||||||
|
YAMP Resource Report Resource Website 1+ mentions |
YAMP (RRID:SCR_016236) | software application, data processing software, data analysis software, software resource, sequence analysis software | Software for processing and analysis of sequencing data. It has a strong focus on quality control, timely processing, functional annotation, and portability. | metagenomics, reproducibility, workflow, containerization, sequencing, gene, rna, annotating, portable, data, process | Free, Available for download | SCR_016236 | YAMP: Yet Another Metagenomic Pipeline, Yet Another Metagenomic Pipeline (YAMP), Yet Another Metagenomic Pipeline | 2026-02-17 10:03:22 | 7 | ||||||||||
|
NIX Resource Report Resource Website 10+ mentions |
NIX (RRID:SCR_016196) | software application, data storage software, software resource, data processing software | Software that defines a data model for annotated scientific datasets. It includes data together with metadata, and a corresponding file format based on HDF5 for storing and sharing such datasets. | data, model, metadata, scientific, integration, file, format, annotation, hdf5, dataset |
uses: Open metadata mark up language is used by: EEGbase has parent organization: German Neuroinformatics Node (G-Node) has parent organization: Ludwig-Maximilians-University; Munich; Germany |
BMBF 01GQ0801; BMBF 01GQ1302 |
DOI:10.3389/conf.fninf.2014.18.00027 | Public | https://fairsharing.org/bsg-s001169 | http://www.g-node.org/nix | SCR_016196 | Pandora, NIX Project | 2026-02-17 10:03:20 | 13 | |||||
|
UTHSCSA ImageTool Resource Report Resource Website 100+ mentions |
UTHSCSA ImageTool (RRID:SCR_016208) | IT | software application, image processing software, data processing software, software resource, image analysis software | Image processing and analysis program for Windows 95 NT and has many of the same capabilities as NIH Image. ImageTool can acquire, display, edit, analyze, process, compress, save and print gray scale and color images. | image, analysis, processing, data, acquisition, compression, modification | has parent organization: University of Texas Health Science Center at San Antonio; Texas; USA | Free, Available for download, Runs on Windows | http://en.bio-soft.net/draw/ImageTool.html | SCR_016208 | UTHSCSA Image Tool, UTHSCSA ImageTool (IT) | 2026-02-17 10:02:40 | 120 | |||||||
|
XLSTAT Resource Report Resource Website 100+ mentions |
XLSTAT (RRID:SCR_016299) | XLSTAT | data management software, software application, data processing software, data analysis software, software resource, data visualization software | Software for commercial data analysis and statistical software package for Microsoft Excel. | data, process, manage, analyze, visualize, graph, statistic, microsoft, excel | is related to: Microsoft Excel | Addinsoft | Commercially available, Trial available | SCR_016299 | XL STATistics | 2026-02-17 10:03:23 | 146 | |||||||
|
TraCeR Resource Report Resource Website 10+ mentions |
TraCeR (RRID:SCR_016338) | software application, data processing software, data analysis software, software resource, software toolkit, simulation software | Software application for recovery of T cell receptor (TCR) data from single cell data. Used to reconstruct full-length, paired T cell receptor (TCR) sequences from T lymphocyte single-cell RNA sequence data. Links T cell specificity with functional response by revealing clonal relationships between cells alongside their transcriptional profiles. | recovery, receptor, single, cell, data, computation, method, reconstruct, sequence, T lymphocyte, RNA, sequence |
is related to: Wellcome Trust Sanger Institute; Hinxton; United Kingdom is related to: European Bioinformatics Institute |
European Research Council ; the Lister Institute for Preventative Medicine (S.A.T.) |
PMID:26950746 | Free, Available for download, Freely available | SCR_016338 | 2026-02-17 10:02:41 | 13 | ||||||||
|
migec Resource Report Resource Website 1+ mentions |
migec (RRID:SCR_016337) | MIGEC | software application, data processing software, data analysis software, software resource, software toolkit | Software package for analysis of immune repertoire sequencing data. Used for recovery of T Cell Receptor ( TCR ) data from bulk population data.Used for high-throughput sequencing data analysis. Allows for error correction while preserving the natural diversity of complex immune repertoires. | high sequencing, molecular, identifier, guided, error, correction, data, analysis, immune, recovery, T cell receptor, | Molecular and Cell Biology program RAS ; Russian Foundation for Basic Research ; Russian President ; European Regional Development Fund |
PMID:24793455 | Free, Available for download, Freely available | SCR_016337 | Molecular Identifier Guided Error Correction | 2026-02-17 10:03:23 | 9 |
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