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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Gsnap2Augustus Resource Report Resource Website 1+ mentions |
Gsnap2Augustus (RRID:SCR_017555) | simulation software, software application, software resource | Software tool to generate hints for Augustus in ab initio gene prediction using 2 step mapping by Gsnap. | Generate, hint, Augustus, gene, prediction, mapping, Gsnap |
uses: GSNAP works with: Augustus |
Free, Available for download, Freely available | SCR_017555 | 2026-08-29 11:27:45 | 1 | ||||||||||
|
Shannon Resource Report Resource Website 1+ mentions |
Shannon (RRID:SCR_017037) | data analysis software, data processing software, software application, software resource | Software tool for de novo transcriptome assembly from RNA-Seq data. | de novo, transcriptome, assembly, RNAseq, data |
has parent organization: University of Washington; Seattle; USA has parent organization: University of California at Berkeley; Berkeley; USA has parent organization: Stanford University; Stanford; California |
NHGRI ; NSF Center for Science of Information ; University of Washington |
Free, Available for download, Freely available | http://sreeramkannan.github.io/Shannon/ | SCR_017037 | 2026-08-29 11:27:43 | 2 | ||||||||
|
NiMARE Resource Report Resource Website 10+ mentions |
NiMARE (RRID:SCR_017398) | NiMARE | data analysis software, data processing software, software application, software resource | Software Python package for coordinate and image based meta analysis of neuroimaging data. | Coordinate, image, based, meta, analysis, neuroimaging, data |
uses: PyMARE is used by: Neurosynth Compose |
Free, Available for download, Freely available | https://nimare.readthedocs.io/en/latest/ | SCR_017398 | Neuroimaging Meta Analysis Research Environment, Neuroimaging Meta-Analysis Research Environment | 2026-08-29 11:27:44 | 17 | |||||||
|
NONMEM Resource Report Resource Website 10+ mentions |
NONMEM (RRID:SCR_016986) | Nonmem | data analysis software, data processing software, simulation software, software application, software resource | Software tool for nonlinear mixed effects modelling. Used for population pharmacokinetic and pharmacodynamic analysis and to simulate data and to fit data. Used in the development of new drugs. NONMEM versions up through 6 are the property of the Regents of the University of California, San Francisco, but ICON Development Solutions has exclusive rights to license their use. NONMEM 7 up to the current version is the property of ICON Development Solutions. | nonlinear, mixed, effect, modeling, pharmacokinetic, pharmacodynamic, analysis, data | is listed by: SoftCite | Commercially available | SCR_016986 | NONMEM 7.4, NONMEM 7, Nonlinear mixed effects modelling software, NONMEM 7.2, NONlinear Mixed Effects Modeling software, population analysis | 2026-08-29 11:27:43 | 45 | ||||||||
|
ngsRelate Resource Report Resource Website 1+ mentions |
ngsRelate (RRID:SCR_016588) | data analysis software, data processing software, software application, software resource | Software tool for estimating pairwise relatedness from next-generation sequencing data. | estimating, pairwise, relatedness, next, generation, sequencing, data, bio.tools, bio.tools |
is listed by: Debian is listed by: bio.tools |
Danish Council for Independent Research ; Danish National Research Foundation |
PMID:26323718 | Free, Available for download, Freely available | biotools:ngsRelateV2, biotools:ngsrelate | https://bio.tools/ngsRelateV2, https://bio.tools/ngsrelate | http://www.popgen.dk/software/index.php?title=NgsRelate&oldid=694 | SCR_016588 | ngsRelateV2 | 2026-08-29 11:28:08 | 6 | ||||
|
ComplexHeatmap Resource Report Resource Website 1000+ mentions |
ComplexHeatmap (RRID:SCR_017270) | data analysis software, data processing software, data visualization software, software application, software resource | Software package to arrange multiple heatmaps and support various annotation graphics. Used to visualize associations between different sources of data sets and to reveal potential patterns. | arrange, multiple, heatmap, visualize, data, pattern, genomic, dataset, bio.tools |
is listed by: Debian is listed by: bio.tools |
BMBF ; German Cancer Research Center-Heidelberg Center for Personalized Oncology |
PMID:27207943 | Free, Available for download, Freely available | biotools:complexheatmap | https://github.com/jokergoo/ComplexHeatmap, https://bio.tools/complexheatmap | SCR_017270 | 2026-08-29 11:28:11 | 3949 | ||||||
|
Computational Structural Biology Toolbox Resource Report Resource Website |
Computational Structural Biology Toolbox (RRID:SCR_016065) | CSB | software library, software resource, software toolkit | Software package as an application framework and a Python class library. It is designed for reading, storing and analyzing biomolecular structures in a variety of formats with rich support for statistical analyses. | software, library, Python, reading, storing, analysis, biomolecular, variety, statistical, analysis, bioinformatic |
is listed by: Debian is listed by: OMICtools |
Deutsche Forschungsgemeinschaft (DFG) grant HA 5918/1-1; Max Planck Society |
PMID:22942023 | Free, Available for download | OMICS_09827 | https://sources.debian.org/src/csb/ | SCR_016065 | Computational Structural Biology Toolbox (CSB), CSB Toolbox | 2026-08-29 11:27:40 | 0 | ||||
|
Seurat Resource Report Resource Website 10000+ mentions |
Seurat (RRID:SCR_016341) | data analysis software, data processing software, software application, software resource, software toolkit | Software R package designed for QC, analysis, and exploration of single cell RNA-seq data. Enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. Used for quality control, analysis, and exploration of single-cell RNA sequencing (scRNA-seq) data. | single, cell, genomic, RNA-seq, data, QC, analysis, source, heterogeneity, transcriptomic, measurement, integrate, diverse |
is used by: Stardust is used by: Seurat MapQuery is used by: scSidekick is related to: DoubletFinder is related to: Azimuth works with: SeuratWrappers works with: Connectome |
NHGRI 1DP2HG009623; NIMH 5R01MH071679; NSF |
PMID:29608179 | Free, Available for download, Freely available | https://satijalab.org/seurat/get_started.html | SCR_016341 | 2026-08-29 11:28:07 | 11480 | |||||||
|
LTRpred Resource Report Resource Website 1+ mentions |
LTRpred (RRID:SCR_017031) | data analysis software, data analytics software, data processing software, software application, software resource | Software package for automated functional annotation of LTR retrotransposons for comparative genomics studies. Used to perform de novo functional annotation of LTR retrotransposons from any genome assembly in fasta format. | LTR, retrotransposon, prediction, genome, assembly, functional, annotation | is related to: R Project for Statistical Computing | Free, Available to download, Freely available | https://hajkd.github.io/LTRpred/ | SCR_017031 | LTRpred(ict) | 2026-08-29 11:27:43 | 6 | ||||||||
|
NIAID Overview of Coronaviruses Resource Report Resource Website 1+ mentions |
NIAID Overview of Coronaviruses (RRID:SCR_018290) | data or information resource, funding resource, portal, topical portal | Information about coronaviruses, including COVID-19. NIAID provides research funding and resources for scientific community to facilitate development of vaccines, therapeutics, and diagnostics for infectious diseases, including those caused by coronaviruses. | Coronavirus, COVID-19, data, infectious disease, NIAID |
is listed by: Data and Computational Resources to Address COVID-19 is related to: NIAID |
COVID-19 | NIAID | Free, Freely available | SCR_018290 | 2026-08-29 11:28:13 | 4 | ||||||||
|
emmeans Resource Report Resource Website 100+ mentions |
emmeans (RRID:SCR_018734) | data analysis software, data analytics software, data processing software, software application, software resource | Software R package to obtain estimated marginal means for linear, generalized linear, and mixed models. Compute contrasts or linear functions of EMMs, trends, and comparisons of slopes. Plots and other displays. | Estimated marginal mean, liner model, mixed model, obtain estimated marginal mean, EMMs, linear function, slope comparison, plot | is related to: CRAN | Free, Available for download, Freely available | https://github.com/rvlenth/emmeans | SCR_018734 | Least Squares Means, Estimated Marginal Means | 2026-08-29 11:27:48 | 195 | ||||||||
|
Diploidocus Resource Report Resource Website 1+ mentions |
Diploidocus (RRID:SCR_021231) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software package for diploid genome assembly analysis. Sequence analysis toolkit for number of different analyses related to diploid genome assembly. | Diploid genome assembly analysis, genome, genome assembly, sequence analysis | uses: DepthSizer | Free, Available for download, Freely available | SCR_021231 | 2026-08-29 11:27:50 | 3 | ||||||||||
|
JUMP Cell Painting Consortium Resource Report Resource Website 1+ mentions |
JUMP Cell Painting Consortium (RRID:SCR_021868) | consortium, data or information resource, organization portal, portal | Consortium is creating new data driven approach to drug discovery based on cellular imaging, image analysis, and high dimensional data analytics. Creates public data set to validate and scale up this image based drug discovery strategy. By coordinating assay procedures across partners, future created data will be well matched. Aims to make cell images as computable as genomes and transcriptomes. | creating new data, drug discovery, cellular imaging, image analysis, high dimensional data analytics, | has parent organization: Broad Institute | Free, Freely available | SCR_021868 | JUMP-Cell Painting Consortium | 2026-08-29 11:27:51 | 2 | |||||||||
|
CytoMAP Resource Report Resource Website 10+ mentions |
CytoMAP (RRID:SCR_021227) | data analysis software, data analytics software, data processing software, software application, software resource, software toolkit | Software tool as spatial analysis software for whole tissue sections.Utilizes information on cell type and position to phenotype local neighborhoods and reveal how their spatial distribution leads to generation of global tissue architecture.Used to make advanced data analytic techniques accessible for single cell data with position information. | Histo cytometric multidimensional, analysis pipeline, whole tissue sections, spatial analysis, single cell data with position information, phenotype local neighborhoods, global tissue architecture | has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA | NIAID R01 AI076327; NIAID R01 AI134246; NIAID R01 AI134713; NIAID R21 AI142667; NIAID T32 AI10667; NIAID U19 AI135976; NICHD T32 HD007233; NIGMS T32 GM007270; NSF DGE 1762114 |
PMID:32320656 | Free, Available for download, Freely available | SCR_021227 | Histo-Cytometric Multidimensional Analysis Pipeline | 2026-08-29 11:28:15 | 23 | |||||||
|
Eco-HAB Resource Report Resource Website |
Eco-HAB (RRID:SCR_021588) | data or information resource, instrument resource, portal, project portal | Portal provides open source, RFID-based system for automated measurement and analysis of social preference and in-cohort sociability in mice. System was developed by Nencki Institute of Experimental Biology scientists. | Instrument, murine social behavior, automated measurement, mice social preference, mice cohort sociability, social preference analysis, OpenBehavior |
is listed by: OpenBehavior has parent organization: Nencki Institute of Experimental Biology; Warsaw; Poland |
DOI:10.7554/elife.19532 | Free, Freely available | SCR_021588 | 2026-08-29 11:28:16 | 0 | |||||||||
|
Oculomatic Eye Tracking project Resource Report Resource Website |
Oculomatic Eye Tracking project (RRID:SCR_021465) | data or information resource, instrument resource, portal, project portal | Project related to investigate mechanisms of oculomotor behavior.Included system is provided by New York University scientists to track eye movement.System includes camera module, lens, IR-Light source, mounting solution, data acquisition device, and general purpose PC. System consists of open source software and modular hardware solution to eye tracking for use in humans and non-human primates. | High speed eye tracking, Point Gray USB3.0 camera, Oculomatic Eye Tracking system, track eye movements, OpenBehavior, Instrument |
is listed by: OpenBehavior is related to: Oculomatic has parent organization: New York University; New York; USA |
DOI:10.1016/j.jneumeth.2016.06.016 | Free, Freely available | SCR_021465 | Oculomatic Eye Tracking | 2026-08-29 11:27:43 | 0 | ||||||||
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M-Track Resource Report Resource Website |
M-Track (RRID:SCR_021508) | data processing software, image analysis software, software application, software resource, software toolkit | Software toolbox for automated detection of forepaw trajectories in mice.Open source code to simultaneously track movement of individual paws during spontaneous grooming episodes and walking in multiple freely behaving mice/rats. | Automated detection, forepaw trajectories, labelled forepaw, freely behaving mice, freely behaving rats, simultaneous trackcking individual paws, movement, spontaneous grooming episodes, OpenBehavior |
is listed by: OpenBehavior is related to: M-Track project |
DOI:10.1371/journal.pcbi.1005115 | Free, Available for download, Freely Available | https://edspace.american.edu/openbehavior/project/m-track/ | SCR_021508 | 2026-08-29 11:27:50 | 0 | ||||||||
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NF Data Portal Resource Report Resource Website 1+ mentions |
NF Data Portal (RRID:SCR_021683) | data or information resource, data repository, portal, service resource, storage service resource | Portal created to help openly explore and share NF datasets, analysis tools, resources, and publications related to neurofibromatosis and schwannomatosis.Public data repository that stores and shares data generated by multiple collaborative research programs focused on neurofibromatosis diseases. | Sage Bionetworks, NF datasets, neurofibromatosis data, schwannomatosis data, neurofibromatosis diseases | uses: Synapse | neurofibromatosis type 1 (NF1), neurofibromatosis type 2 (NF2), and schwannomatosis (SCH) | Childrens Tumor Foundation ; Neurofibromatosis Therapeutic Acceleration Program |
PMID:31836719 | Free, Freely available | r3d100013571 | https://doi.org/10.17616/R31NJMYR | SCR_021683 | Neurofibromatosis Data Portal | 2026-08-29 11:27:51 | 5 | ||||
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Moving Wall Box Resource Report Resource Website |
Moving Wall Box (RRID:SCR_021559) | data or information resource, instrument resource, portal, project portal | Portal provides Moving Wall Box system used to testing strategy task where mouse is repeatedly forced to jump over small ice by slowly moving walls whereby presence of animal is automatically sensed via balances and analyzed by microcontroller board which in turn controls movements of walls. Device provided by Max Planck Institute of Psychiatry scientist. Used for repeated assessment of fear coping strategies. | Instrument, behavioral inhibition, emotional challenging situation, OpenBehavior |
is listed by: OpenBehavior has parent organization: Max-Planck-Gesellschaft |
DOI:10.3389/fnbeh.2017.00201 | Free, Freely available | SCR_021559 | 2026-08-29 11:27:44 | 0 | |||||||||
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Subcellular App Resource Report Resource Website 1+ mentions |
Subcellular App (RRID:SCR_018790) | data access protocol, service resource, software resource, web service | Web interface for simulation of biological molecular networks. Web based environment for creation and simulation of reaction-diffusion models integrated with molecular repository. Allows to import, combine and simulate existing models expressed with BNGL and SBML languages. Application is integrated with number of solvers for reaction-diffusion systems of equations. | Subcellular simulation, reaction-diffusion modeling, brain simulation platform, human brain project, subcellular model, biological molecular network simulation, reaction diffusion model, solver, reaction diffusion system, equation, simulation, molecular network | has parent organization: Human Brain Project EU | Human Brain Project SGA 1-3 | Restricted | SCR_018791 | https://humanbrainproject.github.io/hbp-sp6-guidebook/online_usecases/subcellular_level/subcellular_app/subcellular_app.html | SCR_018790 | Subcellular app, subcellular application, Subcellular Application | 2026-08-29 11:28:14 | 1 |
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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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