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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Mcule Resource Report Resource Website 10+ mentions |
Mcule (RRID:SCR_018921) | portal, web service, data or information resource, data access protocol, software resource | Software drug discovery platform to integrate purchasable chemical space with molecular modeling tools. Chemical marketplace for drug discovery with services based around small molecule compound sourcing. Integrated molecular modeling tools, compound database, IT infrastructure and compound procurement service with web interface. Virtual screens can be run to identify new hits and modeling applications can be used to improve their affinity and other properties. | Drug discovery platform, molecular modeling, molecular modeling tools, compound database, IT infrastructure, compound procurement service, web interface, virtual screening, modeling application | Restricted | SCR_018921 | 2026-08-14 09:28:00 | 46 | |||||||||||
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Hetindel Resource Report Resource Website 1+ mentions |
Hetindel (RRID:SCR_018922) | data processing software, software application, data analysis software, software resource | Software package to identify genomic insertions or deletions, so called indels, in heterozygous sequencing data where both alleles carry mutations. Used to analyze heterozygous indels. | Genomic insertions identification, genomic deletions identification, indel, heterozygous sequencing data, alleles, mutation, heterozygous indel, data | has parent organization: Max Planck Institute for Developmental Biology; Tubingen; Germany | Free, Available for download, Freely available | SCR_018922 | 2026-08-14 09:28:24 | 1 | ||||||||||
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Progenesis QI Resource Report Resource Website 1000+ mentions |
Progenesis QI (RRID:SCR_018923) | data processing software, software application, data analysis software, software resource | Software tool as next generation in LC-MS proteomics data analysis software by Nonlinear Dynamics. | Next generation, LC-MS proteomics data, data analysis, Nonlinear Dynamics | SCR_018923 | 2026-08-14 09:28:08 | 1011 | ||||||||||||
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Chinese Glioma Genome Atlas Resource Report Resource Website 1000+ mentions |
Chinese Glioma Genome Atlas (RRID:SCR_018802) | CGGA | database, topical portal, portal, data or information resource, data set, disease-related portal | Web application for data storage and analysis to explore brain tumors datasets from Chinese cohorts. Data portal for storage and interactive exploration of multi-dimensional functional genomic data that includes primary and recurrent glioma samples from Chinese cohorts. Allows users to browse DNA mutation profile, mRNA/microRNA expression profile and methylation profile, and to do correlation and survival analysis in specific glioma subtype. | Functional genomic data, glioma samples, brain tumor datasets, Chinese cohort, whole exome sequencing data, DNA methylation data, mRNA sequencing data, microRNA microarray data, clinical data, DNA mutation profile analysis, expression profile, methylation profile, survival analysis, glioma subtype, FASEB list | Glioma | DOI:10.1101/2020.01.20.911982 | Free, Freely available | SCR_018802 | 2026-08-14 09:28:24 | 1344 | ||||||||
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TRiCoLOR Resource Report Resource Website 1+ mentions |
TRiCoLOR (RRID:SCR_018801) | data processing software, software application, data analysis software, software resource, sequence analysis software | Command line application for tandem repeats profiling from error prone long read sequencing data. Works on data from Oxford Nanopore Technologies and Pacific Biosciences sequencers. Used on whole genome alignments. | Tandem repeat, long read sequencing data, whole genome alignment, data analysis, sequence analysis, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:tricolor | https://bio.tools/tricolor | SCR_018801 | 2026-08-14 09:27:58 | 2 | ||||||||
|
STAMP Resource Report Resource Website 500+ mentions |
STAMP (RRID:SCR_018887) | software toolkit, data processing software, software application, data analysis software, software resource, data visualization software | Open source software package for analyzing taxonomic or metabolic profiles that promotes best practices in choosing appropriate statistical techniques and reporting results. Graphical software package that provides statistical hypothesis tests and exploratory plots for analyzing taxonomic and functional profiles. Supports tests for comparing pairs of samples or samples organized into two or more treatment groups. | Statistical analysis, taxonomic profile, functional profile, metabolic profile, statistical hypothesis test, plot, sample, sample group, sample pair comparison, bio.tools |
is listed by: Debian is listed by: bio.tools |
Genome Atlantic ; Natural Sciences and Engineering Research Council of Canada ; Australian Research Council ; Canada Foundation for Innovation ; Canada Research Chairs program ; Dalhousie Faculty of Computer Science ; Dalhousie Centre for Comparative Genomics and Evolutionary Bioinformatics ; Tula Foundation Killam Trust |
PMID:25061070 | Free, Freely available | biotools:stamp-metagenomic | https://github.com/dparks1134/STAMP, https://github.com/dparks1134/STAMP/releases, https://bio.tools/stamp-metagenomic | SCR_018887 | STAMP v2.1.3, statistical analysis of taxonomic and functional profiles | 2026-08-14 09:27:59 | 588 | |||||
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Differential Methylation Analysis Package Resource Report Resource Website |
Differential Methylation Analysis Package (RRID:SCR_019148) | DMAP | software toolkit, data processing software, software application, data analysis software, software resource | Software package for large scale genomic DNA methylation analysis. Filters and processes aligned bisulphite sequenced data to generate comprehensive reference methylomes in different units for any genome. Processes aligned SAM files of multiple samples to provide reliable and statistically significant differentially methylated regions, then relate them to proximal genes and CpG features with reasonable rapidity. | Genomic DNA methylation, DNA methylation analysis, bisulphite sequenced data, reference methylomes generation, genome, aligned SAM files processing, differentially methylated regions | has parent organization: University of Otago; Dunedin; New Zealand | National Centre for Growth and Development and Health Research Council ; New Zealand |
PMID:24608764 | Free, Freely available | SCR_019148 | 2026-08-14 09:28:05 | 0 | |||||||
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Toolbox for Representational Similarity Analysis Resource Report Resource Website 1+ mentions |
Toolbox for Representational Similarity Analysis (RRID:SCR_019029) | software toolkit, data processing software, software application, data analysis software, software resource | Software Matlab toolbox to perform representational similarity analysis for neural data. | Representional similarity analysis, data analysis, data, neural data |
is related to: MATLAB has parent organization: University of Cambridge; Cambridge; United Kingdom |
UK Medical Research Council ; European Research Council Starting Grant ; European Research Council Advanced Grant |
PMID:24743308 | Free, Available for download, Freely available | SCR_019029 | RSA toolbox | 2026-08-14 09:28:10 | 9 | |||||||
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Mitoprot Resource Report Resource Website 50+ mentions |
Mitoprot (RRID:SCR_019023) | simulation software, web service, data access protocol, software application, software resource | Web server for prediction of mitochondrial targeting sequences. | Mitochondrial targeting sequence, sequence prediction, mitochondrial sequence, prediction | Free, Freely available | SCR_019023 | 2026-08-14 09:28:26 | 53 | |||||||||||
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Nurses Health Study Resource Report Resource Website 1+ mentions |
Nurses Health Study (RRID:SCR_019144) | data or information resource, portal, topical portal | Portal about prospective investigations into risk factors for major chronic diseases in women. Nurses were selected as study population because of their knowledge about health and their ability to provide complete and accurate information regarding various diseases, due to their nursing education.The largest longitudinal study of women. Started in 1976, involving 275000 participants. | Health Data and Tools | NHS | Free, Freely available | SCR_019144 | Nurses study | 2026-08-14 09:28:12 | 6 | |||||||||
|
LTRharvest Resource Report Resource Website 10+ mentions |
LTRharvest (RRID:SCR_018970) | simulation software, data processing software, software application, data analysis software, software resource | Software tool for de novo detection of full length LTR retrotransposons in large sequence sets. Delivers high quality annotations based on known LTR transposon features like length, distance, and sequence motifs. | De novo detection, full length LTR retrotransposons, retrotransposon, large sequence, annotation, sequence length, sequence distance, sequence motif | has parent organization: University of Hamburg; Hamburg; Germany | PMID:18194517 | https://www.zbh.uni-hamburg.de/en/forschung/gi/software/ltrharvest.html | SCR_018970 | 2026-08-14 09:28:01 | 47 | |||||||||
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Guide Design Resources Resource Report Resource Website 100+ mentions |
Guide Design Resources (RRID:SCR_018982) | organization portal, data or information resource, laboratory portal, portal | Laboratory portal about research including new approaches for precision gene editing, delivery of molecular and genetic cargo, discovery of novel programmable systems, and engineering of immune system to develop next generation of therapeutics. Provides collection of tools for guide design.CRISPR.MIT.EDU of Guide Design Tools is no longer available, documented on August 28,2020. | Guide desin tools, precision gene editing, immune system engineering, next generation therapeutics, guide design | has parent organization: Broad Institute | Free, Freely available | SCR_018982 | 2026-08-14 09:28:09 | 353 | ||||||||||
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IDseq Resource Report Resource Website 10+ mentions |
IDseq (RRID:SCR_019038) | topical portal, production service resource, organism-related portal, portal, data or information resource, service resource, analysis service resource | Open source cloud based pipeline and analysis service for metagenomic pathogen detection and monitoring. Hypothesis free global software platform that helps scientists identify pathogens in metagenomic sequencing data. IDseq Portal accepts raw mNGS data, performs host and quality filtration steps, then executes assembly based alignment pipeline which results in assignment of reads and contigs to taxonomic categories. | Metagenomic pathogen detection, metagenomic pathogen monitoring, identify pathogens, metagenomic sequencing data, data analysis | Chan Zuckerberg Initiative | DOI:10.1101/2020.04.07.030551 | Free, Freely available | https://github.com/chanzuckerberg/idseq-workflows/wiki | SCR_019038 | Infectious Disease Sequencing Platform, IDseq Portal | 2026-08-14 09:28:26 | 30 | |||||||
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CLIP Tool Kit Resource Report Resource Website 10+ mentions |
CLIP Tool Kit (RRID:SCR_019034) | CTK | software toolkit, data processing software, software application, data analysis software, software resource | Software package that provides set of tools for analysis of CLIP data starting from raw reads generated by sequencer. | CLIP data, data analysis, raw reads, sequencer data generation, genome assemblies, data | has parent organization: Columbia University; New York; USA | Free, Available for download, Freely available | SCR_019034 | 2026-08-14 09:28:02 | 22 | |||||||||
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National Collaborative on Childhood Obesity Research Resource Report Resource Website 1+ mentions |
National Collaborative on Childhood Obesity Research (RRID:SCR_019150) | NCCOR | topical portal, portal, data or information resource, disease-related portal, organization portal | Brings together Centers for Disease Control and Prevention, National Institutes of Health, Robert Wood Johnson Foundation, and U.S. Department of Agriculture to accelerate progress in reducing childhood obesity in America, to manage projects and reach common goals, to coordinate funding to make the most of available resources, to share insights and expertise to strengthen research. NCCOR focuses on efforts that have to benefit children, teens, and their families, and communities in which they live. | Childhood obesity, reducing childhood obesity, coordinate funding, coordinate projects, benefit children | Obesity | Free, Freely available | SCR_019150 | 2026-08-14 09:28:13 | 1 | |||||||||
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Agilent MassHunter Qualitative Analysis Resource Report Resource Website 100+ mentions |
Agilent MassHunter Qualitative Analysis (RRID:SCR_019081) | data processing software, software application, data analysis software, data analytics software, software resource | Mass spectrometry screening software for confirmation of target or suspect compounds, and for identification of unknown analytes. Advanced data mining and processing options let find all detectable compounds and confirm targets or identify unknowns. Results can be displayed using data reporting with either preconfigured reports that simplify basic analyses, or completely customized PDF reports. | MassHunter Software, qualitative, mass spectrometry screening, target compound confirmation, unknown analytes identification, data mining, data processing, finding detectable compounds | SCR_019081 | MassHunter Qualitative Analysis | 2026-08-14 09:28:26 | 225 | |||||||||||
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Ventricular Morphometry Analysis System Resource Report Resource Website |
Ventricular Morphometry Analysis System (RRID:SCR_019007) | VMAS | data processing software, software application, data analysis software, software resource | Software tool to generate whole connected 3D brain ventricular shape model and encode ventricular surface deformation information that is inaccessible by ventricle volume measure. Contains automated segmentation approach and surface based multivariate morphometry statistics. | 3D brain model generation, 3D brain, ventricular shape model, ventricular surface deformation encoding, ventricle volume measure, automated segmentation, multivariate morphometry statistics, analysis system |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Arizona State University; Arizona; USA |
Free, Available for download, Freely available | http://gsl.lab.asu.edu/software/ventricle/ | SCR_019007 | 2026-08-14 09:28:02 | 0 | ||||||||
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OpenCOR Resource Report Resource Website 1+ mentions |
OpenCOR (RRID:SCR_019001) | software application, simulation software, software resource | Open source cross platform modeling environment for reproducible science. Used to organise, edit, simulate and analyse models described in CellML format, using SED-ML and COMBINE archives. | Modeling environment, reproducible science, CellML format model, CellML format model analysis, CellML format model simulation |
uses: Simulation Experiment Description Markup Language is used by: SPARC Portal |
Free, Available for download, Freely available | SCR_019001 | 2026-08-14 09:28:02 | 6 | ||||||||||
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datasets.datalad.org Resource Report Resource Website 1+ mentions |
datasets.datalad.org (RRID:SCR_019089) | data repository, storage service resource, data or information resource, data set, service resource | DataLad data distribution. Super dataset collating DataLad datasets from various sources including OpenNeuro, CRCNS, etc., to provide unified access to over 200TB of neural data. | Version control system, data distribution, super dataset, DataLad dataset, neural data | is related to: DataLad | NSF 1429999; NSF 1912266; NIBIB P41 EB019936 |
Free, Freely available | https://www.datalad.org/datasets.html | SCR_019089 | 2026-08-14 09:28:11 | 8 | ||||||||
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HADDOCK Resource Report Resource Website 100+ mentions |
HADDOCK (RRID:SCR_019091) | simulation software, web service, data access protocol, software application, software resource | Software tool as information driven flexible docking approach for modeling of biomolecular complexes.User friendly integrative modeling of biomolecular complexes.HADDOCK v 2.2 offers new features such as support for mixed molecule types, additional experimental restraints and improved protocols, all of this in user friendly interface. | Molecular docking, data driven, biomolecular complex, grid computing, hybrid modeling, protein complex | has parent organization: Utrecht University; Utrecht; Netherlands | PMID:12580598 PMID:26410586 |
Restricted | https://www.bonvinlab.org/software/haddock2.2/, https://wenmr.science.uu.nl/haddock2.4/ | SCR_019091 | HADDOCK2.2, HADDOCK2.4, High Ambiguity Driven protein-protein DOCKing | 2026-08-14 09:28:03 | 168 |
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