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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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cRAP protein sequences Resource Report Resource Website 100+ mentions |
cRAP protein sequences (RRID:SCR_018187) | cRAP | data or information resource, data repository, database, service resource, storage service resource | List of proteins commonly found in proteomics experiments that are present either by accident or through unavoidable contamination of protein samples. List is based on analysis of current version of GPMDB, as well as suggestions by users. Current version of cRAP in FASTA format can be obtained from the GPM FTP site. | Protein, collection, proteomic experiment, protein sample, contamination, Global Proteome Machine Data Base, data repository, data, FASEB list | THIS RESOURCE IS NO LONGER IN SERVICE | ftp://ftp.thegpm.org/fasta/cRAP | SCR_018187 | SciCrunch Registry | common Repository of Adventitious Proteins | 2026-09-26 02:17:16 | 198 | ||||||||
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Loupe Browser Resource Report Resource Website 100+ mentions |
Loupe Browser (RRID:SCR_018555) | data analysis software, data processing software, software application, software resource | Desktop application that provides interactive visualization functionality to analyze data from different 10x Genomics solutions. Used to interrogate different views of 10x data to gain insights into underlying biology. | Interactive visualization, data analysis, 10x Genomics solutions, data | works with: Cell Ranger | Restricted | SCR_018555 | SciCrunch Registry | Loupe Cell Browser 4.0 | 2026-09-26 02:17:18 | 187 | |||||||||
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Coronavirus Immunotherapy Consortium Resource Report Resource Website 10+ mentions |
Coronavirus Immunotherapy Consortium (RRID:SCR_018258) | CoVIC | consortium, data or information resource, organization portal, portal, topical portal | Consortium to unite efforts and resources from experts across globe to advance effective, antibody based therapies against novel coronavirus, SARS-CoV-2. Represents multidisciplinary convergence of structural biology, virologists, immunologists, clinicians and bioinformaticians from academic and industry settings. Collects antibodies for testing as part of CoVICS. Contributed antibodies are blinded and will only be known as code name. Antibody contributors will be able to see performance of their own molecules and take part in analysis. Contributors retain ownership of their antibodies and may continue to publish on them using original antibody names. Goal is to determine relative in vitro potency and in vivo efficacy using centralized standardized assays to identify best individual mAbs and rational combinations of mAbs. Consortium will recommend ideal therapeutic molecules for human use to protect vulnerable populations from COVID-19 disease. CoVIC database (CoVIC-DB) will serve as clearinghouse for monoclonal antibodies against SARS-CoV-2. Database will catalog contributed antibodies in searchable resource and provide interactive analysis tools for comparisons among them. | COVID-19, antibody, antibody based therapy, coronavirus, SARS-CoV-2, antibody collection, analysis, potency in vitro, efficacy in vivo, standardized assay, identify mAb, therapeutic molecule, vulnerable population protect, database, data |
is related to: La Jolla Institute for Immunology is related to: Duke University; North Carolina; USA is related to: CoVIC-DB Database |
COVID-19 | Free, Freely available | SCR_018258 | SciCrunch Registry | 2026-09-26 02:17:18 | 14 | ||||||||
|
METAGENOTE Resource Report Resource Website 1+ mentions |
METAGENOTE (RRID:SCR_018494) | data access protocol, software resource, web service | Quick and intuitive way to annotate data from genomics studies including microbiome. Project to aid researchers in applying standardized metadata describing what, where, how, and when of samples collected in genomics study. Collection of METAdata of GEnomics studies on web based NOTEbook. Metadata are stored in centralized repository and validated according to guidelines from Genomics Standard Consortium, which are also supported by repositories and large microbiome initiatives such as NCBI, European Bioinformatics Institute (EBI), and Earth Microbiome Project. Upon request from researchers, data will also be submitted for publication via NCBI Sequence Read Archive (SRA) repository. | Annotate data, genomics study, microbiome, metadata, genomics, data |
is related to: NCBI Sequence Read Archive (SRA) is related to: NCBI |
NIH | Free, Freely available | SCR_018494 | SciCrunch Registry | METAdata of GEnomics studies on a web based NOTEbook | 2026-09-26 02:17:16 | 1 | ||||||||
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Stanford University Human Immune Monitoring Center Core Facility Resource Report Resource Website 1+ mentions |
Stanford University Human Immune Monitoring Center Core Facility (RRID:SCR_018266) | HIMC | access service resource, core facility, data or information resource, service resource | Core designed for immune monitoring services for clinical and translational studies. Goals include providing standardized, state-of-the art immune monitoring assays at RNA, protein, and cellular level, testing and developing new technologies for immune monitoring, archive, report, and mine data from immune monitoring studies. HIMC uses online database for integration of data from standard HIMC assays, along with de-identified clinical and demographic data. | Immune monitoring serivce, clinical study, translational study, RNA, protein, data, core facility, USEDit, ABRF |
is listed by: ABRF CoreMarketplace is related to: USEDit has parent organization: Stanford University; Stanford; California |
Open | ABRF_399 | https://coremarketplace.org/?FacilityID=399 | SCR_018266 | SciCrunch Registry | Stanford University - Human Immune Monitoring Center, Human Immune Monitoring Center (HIMC) | 2026-09-26 02:17:16 | 1 | ||||||
|
ClusPro Resource Report Resource Website 500+ mentions |
ClusPro (RRID:SCR_018248) | data access protocol, service resource, software resource, web service | Web tool for protein-protein docking. Server provides removal of unstructured protein regions, application of attraction or repulsion, accounting for pairwise distance restraints, construction of homo-multimers, consideration of small-angle X-ray scattering data, and location of heparin-binding sites. Six different energy functions can be used, depending on protein type.This protocol describes use of various options, construction of auxiliary restraints files, selection of energy parameters, and analysis of results. | Protein-protein docking, protein structure, energy function, energy parameter selection, analysis, data |
has parent organization: Boston University; Massachusetts; USA has parent organization: Stony Brook University; New York; USA |
NIGMS R01 GM061867; NIGMS R35 GM118078 |
PMID:28079879 | Free, Freely available | SCR_018248 | SciCrunch Registry | ClusPro 2.0 | 2026-09-26 02:17:16 | 979 | |||||||
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Redivis Resource Report Resource Website 10+ mentions |
Redivis (RRID:SCR_023111) | Redivis | data repository, service resource, software repository, software resource, storage service resource | Commercial collaborative research platform for hosting and analyzing datasets.Data platform for academic research. Redivis provides organizations with central hub where researchers can easily discover, access, and analyze their data. | Data platform, central hub, discover, access, analyze, data, academic research, hosting datasets, analyzing datasets | is related to: DataCite | Restricted | r3d100014398, 10.57761, SCR_024550 | https://search.datacite.org/repositories/sul.swbvyu, https://doi.org/10.57761/, https://dx.doi.org/10.57761, https://doi.org/10.17616/R31NJNLQ | SCR_023111 | SciCrunch Registry | Red Vis | 2026-09-26 02:17:26 | 14 | ||||||
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Allen Brain Atlas Tools Resource Report Resource Website |
Allen Brain Atlas Tools (RRID:SCR_023855) | ABAT | software resource | Software stores mutiple MATLAB functions to read, analyze, and visualize various kinds of data from Allen Brain Atlas. | Allen Human Brain Atlas, MATLAB functions, Allen Brain Atlas data, data, read, analyze, visualize | is related to: Allen Institute for Brain Science | Free, Freely available | SCR_023855 | SciCrunch Registry | ABAT (Allen Brain Atlas Tools) | 2026-09-26 02:17:31 | 0 | ||||||||
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EarthCube Resource Report Resource Website 1+ mentions |
EarthCube (RRID:SCR_024576) | data or information resource, portal, topical portal | Platform provides tools, data, services, apps and community resources for geoscience researchers. EarthCube community works together to influence how data will be collected accessed, analyzed, visualized, shared and archived; participate in interdisciplinary and collaborative research; and contribute to transformation of geoscience research through emerging practices of digital scholarship, data and software stewardship, and open science. | open science, geoscience, geoscience interdisciplinary and collaborative research, tools, data, services, apps, community resources, |
is listed by: DataCite has parent organization: University of California; California; USA |
Free, Freely available | https://api.datacite.org/dois?prefix=10.25352 | SCR_024576 | SciCrunch Registry | 2026-09-26 02:17:36 | 1 | |||||||||
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California Coastal Atlas Resource Report Resource Website |
California Coastal Atlas (RRID:SCR_024554) | data or information resource, portal, topical portal | Resource designed to publish information and data about California coast reflecting current scientific understanding and data for the purpose of informing public policy and advancing the understanding of coastal processes. | California coast, water, climate, coastal processes, data, informing public policy, |
is listed by: DataCite has parent organization: University of California; California; USA |
Free, Freely available | https://api.datacite.org/dois?prefix=10.4246 | SCR_024554 | SciCrunch Registry | 2026-09-26 02:17:36 | 0 | |||||||||
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Cerner Enviza Resource Report Resource Website |
Cerner Enviza (RRID:SCR_024435) | commercial organization | American healthcare company that provides data, analytics, and research to the life sciences industry, with particular focus on oncology and rare diseases. | Oracle, Cerner, data, analytics, oncology, rare disease, | SCR_024435 | SciCrunch Registry | 2026-09-26 02:17:35 | 0 | ||||||||||||
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Sanford Burnham Prebys Medical Discovery Institute Bioinformatics and Data Management Facility Resource Report Resource Website |
Sanford Burnham Prebys Medical Discovery Institute Bioinformatics and Data Management Facility (RRID:SCR_014868) | SBP MDI Bioinformatics and Data Management Facility, SBP Medical Discovery Institute Bioinformatics and Data Management Facility, SBP MDI Bioinformatics and Data Management Facility | access service resource, computational hosting, core facility, group, service resource, software resource, training core facility | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on 11132025. Facility that provides database development and management and bioinformatic network building services by utilizing on-site hardware and software. Three members of the facility are available to assist researchers with advanced bioinformatics and biostatistics analysis to help put data into biological context across various disease areas to create testable hypotheses and understand biology of the process. The bulk of support includes connecting functional genomic data with pathways and networks, connecting gene/protein expression and disease state and consultations on statistical aspects of the research with the team statistician. | data, management, database, bioinformatic, network, connectivity, statistics, analysis, biostatistics, pipeline, software | THIS RESOURCE IS NO LONGER IN SERVICE. | SCR_014868 | SciCrunch Registry | SBP, , Data Management Facility, MDI, Medical Discovery Institute, Sanford Burnham Prebys, Bioinformatics | 2026-09-26 02:15:29 | 0 | |||||||||
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MetaboAnalyst Resource Report Resource Website 10000+ mentions |
MetaboAnalyst (RRID:SCR_015539) | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | Web server for statistical, functional and integrative analysis of metabolomics data. Web based tool suite used for metabolomic data processing, normalization, multivariate statistical analysis, and data annotation, biomarker discovery and classification. | statistical, functional, integrative, analysis, metabolomics, data, processing, annotation, biomarker, discovery |
is listed by: SoftCite has parent organization: McGill University; Montreal; Canada has parent organization: University of Alberta; Alberta; Canada |
Alberta Ingenuity Fund ; Alberta Life Sciences Institute ; Canada Research Chairs Program ; Canadian Institutes for Health Research ; Genome Alberta ; Genome Canada ; McGill University ; Natural Sciences and Engineering Research Council of Canada |
PMID:29762782 | Free, Available for download, Freely available, Tutorial available, Acknowledgement requested | SCR_016717 | http://old.metaboanalyst.ca/MetaboAnalyst/ | SCR_015539 | SciCrunch Registry | MetaboAnalyst 4.0, MetaboAnalyst 3.0 | 2026-09-26 02:15:34 | 13689 | |||||
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Autogrid Resource Report Resource Website 1000+ mentions |
Autogrid (RRID:SCR_015982) | data analysis software, data processing software, simulation software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2023.Software for automated docking analysis to precalculate the set of grids describing the target protein. It is a part of automated molecular modeling simulation software AutoDock. | software, automated, docking, analysis, tool, precalculate, set, grid, ligand, protein, target, molecular, simulation, modeling, protein-ligand interaction, data |
is listed by: SoftCite is related to: AutoDock has parent organization: The Scripps Research Institute Labs and Facilities |
The Scripps Research Institute ; San Diego ; California |
PMID:16862531 | THIS RESOURCE IS NO LONGER IN SERVICE | http://mgl.scripps.edu/forum | SCR_015982 | SciCrunch Registry | Autogrid toolkit, Autogrid: automated grid | 2026-09-26 02:15:40 | 1261 | ||||||
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Bamtools Resource Report Resource Website 100+ mentions |
Bamtools (RRID:SCR_015987) | data analysis software, data management software, data processing software, software application, software resource, software toolkit | Software that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating genome sequence alignment files in the BAM and SAM formats. It is used for research analysis and management of data produced by sequencing technologies. | c++, api, sam, bam genome, sequence, alignment, data, analysis, management, command, manipulation, binary, map, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
NHGRI R01 HG004719; NHGRI RC2 HG005552 |
PMID:21493652 DOI:10.1093/bioinformatics/btr174 |
biotools:bamtools, OMICS_11315 | https://bio.tools/bamtools, https://sources.debian.org/src/bamtools/ | SCR_015987 | SciCrunch Registry | API:Application Programming Interface, BAM:Binary Alignment Map, SAM:Sequence Alignment Map | 2026-09-26 02:15:40 | 344 | ||||||
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Blixem Resource Report Resource Website 1+ mentions |
Blixem (RRID:SCR_015994) | alignment software, data processing software, image analysis software, software application, software resource | Software for sequence alignments that displays multiple match sequences aligned against a single genomic reference sequence. It can be used for manipulation, display and annotation of genomic data, to check the quality of an alignment, to find missing/misaligned sequence, and to identify splice sites and polyA sites. | software, sequence, alignment, annotation, genomic, reference, data, display, manipulation, DNA |
is related to: SEQtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
NHGRI U54 HG00455; Wellcome Trust Grant 098051 |
PMID:26801397 | Free, Available for download | SCR_015994 | SciCrunch Registry | SEQtools Blixem | 2026-09-26 02:15:40 | 2 | |||||||
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auto-scoring Resource Report Resource Website |
auto-scoring (RRID:SCR_016015) | data processing software, data visualization software, software application, software resource | Visualization software that calculates derived scores for the electronic record system REDCap (Research Electronic Data Capture) to build and manage online surveys and databases. Used in the ABCD-STUDY (Adolescent Brain Cognitive Development - STUDY) report framework. | visual, data, processing, calculate, derived, score, electronic, record, system, data, capture, research | is related to: University of California at San Diego; California; USA | NIDA U24 DA041123 | Free, Available for download | SCR_016015 | SciCrunch Registry | 2026-09-26 02:15:40 | 0 | |||||||||
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little-man-task Resource Report Resource Website |
little-man-task (RRID:SCR_016018) | data management software, data processing software, data transfer software, software application, software resource | Software tool to manage data and derived results. It is used for import of derived measures into REDCap (Research Electronic Data Capture). | capture, data, manage, derive, measure, abcd, study | is related to: University of California at San Diego; California; USA | NIDA U24 DA041123 | Free, Available for download | SCR_016018 | SciCrunch Registry | 2026-09-26 02:15:40 | 0 | |||||||||
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redcap-completion Resource Report Resource Website |
redcap-completion (RRID:SCR_016019) | data management software, software application, software resource | Software to measure item level completion in a large REDCap project. It provides a web-interface to review data and it is used in the ABCD project to assess data collection sites for the reached level of completion. | measure, item, level, completion, large, electronic, data, capture, research, review, data, collection |
is related to: University of California at San Diego; California; USA works with: REDCap |
NIDA U24 DA041123 | Free, Available for download | SCR_016019 | SciCrunch Registry | 2026-09-26 02:15:40 | 0 | |||||||||
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aux-file-upload Resource Report Resource Website |
aux-file-upload (RRID:SCR_016026) | data management software, data processing software, data transfer software, software application, software resource | Software application to upload functional MR imaging runs produce auxilary data that can be collected centrally. Connects to a subject database research electronic data capture (REDCap). | upload, data, transmitted, addition, basic, calculation, subject, database, research, electronic, capture, imaging, session, abcd |
is related to: University of California at San Diego; California; USA works with: ABCD Study works with: REDCap |
NIDA U24 DA041123 | Free, Available for download | SCR_016026 | SciCrunch Registry | 2026-09-26 02:15:40 | 0 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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