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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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AssayZap Resource Report Resource Website 10+ mentions |
AssayZap (RRID:SCR_016991) | software application, data processing software, software resource | Software tool as universal assay calculator for RIA, ELISA, IRMA, colorimetric or any other type of assay by Biosoft. Maintains record for each assay, and enables standard curve and QCs to be compared and adjusted. Can process data from 96 and 384-well plate readers in any order. | assay, calculator, RIA, ELISA, IRMA, Biosoft, data, process | Commercially available | SCR_016991 | 2026-02-15 09:21:13 | 15 | |||||||||||
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hMRI-toolbox Resource Report Resource Website 10+ mentions |
hMRI-toolbox (RRID:SCR_017682) | software application, data processing software, software toolkit, software resource | Software toolbox for quantitative MRI in neuroscience and clinical research. Open source and flexible tool for qMRI data handling and processing. Allows estimation of high quality multi parameter qMRI maps followed by spatial registration in common space for statistical analysis. | Quantitative, MRI, data, processing, multi, parameter, qMRI, map, spatial, registration, statistical, analysis, histology, longitudinal, relaxation, rate R1 and R2, proton, density, magnetisation, transfer, MT saturation |
is related to: MATLAB is related to: SPM |
European Structural and Investment Fund ; European Regional Development Fund ; Belgian Walloon Government ; European Research Council ; Swiss State Secretariat for Education ; Research and Innovation ; German Research Foundation ; Swiss National Science Foundation ; Leenaards Foundation ; Roger De Spoelberch Foundation ; Wellcome Trust ; Emory Universitys Research Council ; Swedish Research Council |
DOI:10.1016/j.neuroimage.2019.01.029 | Free, Available for download, Freely available | https://github.com/hMRI-group/hMRI-toolbox | SCR_017682 | 2026-02-15 09:22:12 | 33 | |||||||
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Scmap Resource Report Resource Website 10+ mentions |
Scmap (RRID:SCR_017338) | software application, data processing software, software resource | Software tool for unsupervised projection of single cell RNA-seq data. Used for projecting cells from scRNA-seq data set onto cell types or individual cells from other experiments. | Unsupervised, projection, single, cell, RNA-seq, data |
is listed by: Bioconductor has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:29608555 | Free, Available for download, Freely available | http://bioconductor.org/packages/scmap/ https://www.sanger.ac.uk/science/tools/scmap |
SCR_017338 | 2026-02-15 09:21:19 | 15 | ||||||||
|
FlowCal Resource Report Resource Website 1+ mentions |
FlowCal (RRID:SCR_018140) | software application, data processing software, software resource | Open source software tool for automatically converting flow cytometry data from arbitrary to calibrated units. Can be run using intuitive Microsoft Excel interface, or customizable Python scripts. Software accepts Flow Cytometry Standard (FCS) files as inputs and is compatible with different calibration particles, fluorescent probes, and cell types. Automatically gates data, calculates common statistics, and produces plots. | Converting flow cytometry data, arbitrary unit, calibrated unit, data gating, statistic, plot, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
NSF EFRI 1137266; NSF MCB 1244135; Office of Naval Research MURI N000141310074; Office of Naval Research YIP N000141410487; NIAID R21 AI115014; Welch Foundation ; NSF Graduate Research Fellowship DGE 0940902; NDSEG Fellowship |
PMID:27110723 | Free, Available for download, Freely available | biotools:flowcal | https://bio.tools/flowcal | SCR_018140 | Python Flow Cytometry Calibration Library | 2026-02-15 09:22:11 | 5 | |||||
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Neuron Tools Resource Report Resource Website 1+ mentions |
Neuron Tools (RRID:SCR_017450) | software application, data processing software, software resource | Software tools for converting data files into persistence diagrams and distance matrices. | Converting, data, file, diagram, distance, matice, BRAIN Initiative | is recommended by: BRAIN Initiative | NIBIB EB022899 | Free, Available for download, Freely available | SCR_017450 | 2026-02-15 09:22:06 | 3 | |||||||||
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NanoFilt Resource Report Resource Website 100+ mentions |
NanoFilt (RRID:SCR_016966) | software application, data processing software, software resource | Software tool written in Python to perform its filtering based on mean read quality and GC content and read length. Used for filtering and trimming of long read sequencing data. | filtering, trimming, long, sequencing, data, read |
is listed by: OMICtools is listed by: Debian |
Free, Available for download, Freely available | https://sources.debian.org/src/nanofilt/ | SCR_016966 | 2026-02-15 09:21:52 | 268 | |||||||||
|
ScaffMatch Resource Report Resource Website 1+ mentions |
ScaffMatch (RRID:SCR_017025) | software application, data processing software, software resource | Software tool as scaffolding algorithm based on maximum weight matching able to produce high quality scaffolds from next generation sequencing data (reads and contigs). Able to handle reads with both short and long insert sizes. | scaffolding, algorithm, maximum, weight, matching, next, generation, sequencing, data, read, contig, bio.tools |
uses: Python Programming Language is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Georgia State University; Georgia; USA |
NSF IIS 0916401 | PMID:25890305 | Free, Available for download, Freely available | biotools:scaffmatch, OMICS_08198 | http://alan.cs.gsu.edu/NGS/?q=content/scaffmatch https://bio.tools/scaffmatch |
SCR_017025 | 2026-02-15 09:21:54 | 1 | ||||||
|
BASTA Resource Report Resource Website 1+ mentions |
BASTA (RRID:SCR_017303) | software application, data processing software, software toolkit, software resource | Software package as Bayesian method to infer migration from genetic data. Implemented in BEAST2 that combines accuracy of methods based on structured coalescent with computational efficiency required to handle more than few populations. | Bayesian method, infer, migration, genetic, data, structured, coalescent, approximation, population | is related to: BEAST2 | DOI:10.1371/journal.pgen.1005421 | Free, Available for download, Freely available | SCR_017303 | BAyesian STructured coalescent Approximation, BASTA, BEAST2 | 2026-02-15 09:22:02 | 1 | ||||||||
|
Science of Behavior Change Research Network Resource Report Resource Website |
Science of Behavior Change Research Network (RRID:SCR_017385) | SOBC | project portal, data or information resource, portal | Repository for behavioral science measures that have been validated or are in process of being validated in accordance with SOBC Experimental Medicine Approach. | Data, behavioral, science, SOBC, measure, data, medicine | NIH | SCR_017388 | https://scienceofbehaviorchange.org/measures/ https://scienceofbehaviorchange.org/measures/ |
SCR_017385 | SOBC Measures Repository, Science of Behavior Change (SOBC) Research Network | 2026-02-15 09:22:01 | 0 | |||||||
|
GEOMAGIC Studio Resource Report Resource Website 1+ mentions |
GEOMAGIC Studio (RRID:SCR_016978) | GEOMAGIC Studio 12 | software application, data processing software, software resource | Software tool to convert 3D scans into parametric models. Transforms 3D scan data into highly accurate surface, polygon and native CAD models. Used for reverse engineering, product design, rapid prototyping and analysis. | 3D, scan, convert, data, surface, polygon, native, CAD, model | Free, Available for download, Freely available | https://de.3dsystems.com/press-releases/geomagic/studio-12-offers-fastest-way-to-convert-3d-scans-of-phy | SCR_016978 | 2026-02-15 09:21:13 | 1 | |||||||||
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Mnemiopsis Genome Project Portal Resource Report Resource Website |
Mnemiopsis Genome Project Portal (RRID:SCR_018293) | MGP Portal | project portal, data or information resource, portal | Portal to obtain genomic information on Mnemiopsis. Data available provide annotations and other key biological information not available elsewhere. Used to advance research projects aimed at understanding phylogenetic diversity and evolution of proteins that play fundamental role in metazoan development. Collection of sequenced, assembled, annotated, and performed preliminary analysis of genome of Mnemiopsis. | Genomic, data, metazoan development, Mnemiopsis leidyi, Ctenophore, moel organisms, genomic data analysis |
is related to: University of Michigan; Ann Arbor; USA is related to: Brown University; Rhode Island; USA is related to: University of Florida; Florida; USA |
Free, Freely available | SCR_018293 | 2026-02-15 09:21:35 | 0 | |||||||||
|
Hierarchical Data Modeling Framework Resource Report Resource Website 1+ mentions |
Hierarchical Data Modeling Framework (RRID:SCR_021303) | HDMF | software application, data processing software, software toolkit, software resource | Open source software Python package for working with hierarchical data. Provides APIs for specifying data models, reading and writing data to different storage backends, and representing data with Python object.Used for working with standardizing, reading, and writing hierarchical object data. | Hierarchical data, data models, reading data, writing data, unified data format, different storage backends, Python object, data, data standards |
is used by: PyNWB is related to: Neurodata Without Borders is related to: Neurodata Extensions Catalog is related to: HDMF Documentation Utilities is related to: HDMF Common Schema |
DOI:10.1109/BigData47090.2019.9005648 | Free, Available for download, Freely available | SCR_021303 | 2026-02-15 09:22:32 | 1 | ||||||||
|
viral_seq Resource Report Resource Website 1+ mentions |
viral_seq (RRID:SCR_018515) | software application, data processing software, software resource | Ruby Gem with bioinformatics tools for processing viral NGS data. Specifically for Primer-ID sequencing and HIV drug resistance analysis. | Processing viral data, next generation sequencing data, viral data, sequencing, HIV drug resistance analysis, Primer ID sequencing, data | Free, Available for download, Freely available | https://github.com/ViralSeq/viral_seq | SCR_018515 | 2026-02-15 09:21:38 | 2 | ||||||||||
|
EphysExtraction Resource Report Resource Website 1+ mentions |
EphysExtraction (RRID:SCR_018193) | software application, data processing software, software resource | Software tool as code to extract electrophysiological parameters of neurons. Code is continuously being updated to handle more kinds of voltage traces and extract different kinds of features. | electrophysiological parameter, extract parameter, neuron parameter, voltage trace, data | Free, Available for download, Freely available | SCR_018193 | 2026-02-15 09:22:11 | 2 | |||||||||||
|
GeneSyntenyPipeline Resource Report Resource Website |
GeneSyntenyPipeline (RRID:SCR_018198) | software application, data processing software, software resource | Software pipeline was designed to draw gene synteny plot between genomes and obtain 1 to 1 gene pairs from each genome. | Genome, synteny, plot, JCVI, gene pair, data | Free, Available for download, Freely available | SCR_018198 | 2026-02-15 09:21:33 | 0 | |||||||||||
|
DecodingDynamic Resource Report Resource Website 1+ mentions |
DecodingDynamic (RRID:SCR_021099) | data or information resource, source code, software resource | Data, code, and notebooks for replicating analyses reported in Rogers et al., Evidence for deep, distributed and dynamic semantic code in human ventral anterior temporal cortex. | ECoG, neural networks, semantics, replicating analyses, data, code, notebooks, human ventral anterior temporal cortex, semantic code | Medical Research Council Programme ; European Research Council |
DOI:10.1101/695049 | Free, Freely available | SCR_021099 | 2026-02-15 09:21:57 | 1 | |||||||||
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CustomCDF Resource Report Resource Website 1+ mentions |
CustomCDF (RRID:SCR_018527) | software application, data processing software, software resource | Brainarray custom CDFs for processing raw Affymetrix data. Used to map probe to probesets. Oligonucleotide probes on GeneChips are reorganized based on latest genome and transcriptome information. | Brainarray, custom CDF, processing raw Affymetrix data, data processing, map probe, probset, oligonucleotide probe, GeneChips, genome, transcriptome, data | PMID:16284200 | Free, Freely available | https://gist.github.com/rmflight/3108891 https://rdrr.io/github/jakejh/metapredict/man/installCustomCdfPackages.html |
SCR_018527 | 2026-02-15 09:22:22 | 8 | |||||||||
|
OpenNeuro Resource Report Resource Website 100+ mentions |
OpenNeuro (RRID:SCR_005031) | OpenNeuro, OpenfMRI | database, service resource, storage service resource, data repository, data or information resource, image repository | Open platform for analyzing and sharing neuroimaging data from human brain imaging research studies. Brain Imaging Data Structure ( BIDS) compliant database. Formerly known as OpenfMRI. Data archives to hold magnetic resonance imaging data. Platform for sharing MRI, MEG, EEG, iEEG, and ECoG data. | neuroinformatics, database, storing, dataset, neuroimaging, data, MRI, MEG, EEG, iEEG, ECoG, FASEB list |
uses: Brain Imaging Data Structure (BIDs) uses: HED Tags is used by: studyforrest.org is used by: DataLad is used by: NIF Data Federation is used by: Integrated Datasets is used by: NIH Heal Project is used by: Baby Open Brains is recommended by: National Library of Medicine is recommended by: BRAIN Initiative is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: re3data.org is listed by: DataCite is listed by: FAIRsharing is affiliated with: NEMAR is related to: Integrated Manually Extracted Annotation has parent organization: Stanford University; Stanford; California has parent organization: Stanford Center for Reproducible Neuroscience has parent organization: BRAIN Initiative is provided by: OpenNeuro |
NSF OCI1131441; NIDA ; Laura and John Arnold Foundation ; Stanford ; Squishymedia ; BRAIN Initiative ; NIMH |
Free, Freely available | DOI:10.25504/FAIRsharing.s1r9bw, r3d100010924, nlx_144048, DOI:10.17616/R33047, DOI:10.18112 | http://www.nitrc.org/projects/openfmri https://github.com/OpenNeuroDatasets https://doi.org/10.17616/R33047 https://doi.org/10.17616/r33047 https://doi.org/10.18112/ https://dx.doi.org/10.18112/ https://fairsharing.org/10.25504/FAIRsharing.s1r9bw https://doi.org/10.17616/R33047 |
http://openfmri.org | SCR_005031 | OpenfMRI, Open fMRI, OpenNeuro | 2026-02-15 09:18:53 | 247 | ||||
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UCSC Genome Browser Resource Report Resource Website 10000+ mentions Rating or validation data |
UCSC Genome Browser (RRID:SCR_005780) | portal, database, service resource, project portal, data or information resource | Portal to interactively visualize genomic data. Provides reference sequences and working draft assemblies for collection of genomes and access to ENCODE and Neanderthal projects. Includes collection of vertebrate and model organism assemblies and annotations, along with suite of tools for viewing, analyzing and downloading data. | Reference, sequence, assembly, collection, genome, visualize, genomic, data, ENCODE, Neanderthal, project, sequencing |
is used by: VizHub is used by: Blueprint Epigenome is used by: QmRLFS-finder is used by: International Human Epigenome Consortium Data Portal is used by: iPiG is listed by: re3data.org is listed by: OMICtools is listed by: Educational Resources in Neuroscience is listed by: SoftCite is related to: HEXEvent is related to: PicTar is related to: Phenotree is related to: Enhancer Trap Line Browser is related to: CistromeFinder is related to: ENCODE is related to: Human Epigenome Atlas is related to: ENCODE is related to: BigWig and BigBed is related to: PhenCode is related to: doRiNA is related to: ISCA Consortium is related to: WashU Epigenome Browser is related to: CRISPOR is related to: liftOver is related to: kent has parent organization: University of California at Santa Cruz; California; USA works with: TarBase |
UC BIOTEuropean UnionH ; Alfred P. Sloan Foundation ; David and Lucille Packard Foundation ; NIH ; HHMI ; CISI ; NHGRI ; DOE ; NSF DBI 9809007; NIGMS GM52848 |
PMID:12045153 PMID:22908213 PMID:23155063 |
OMICS_00926, SCR_017502, nif-0000-03603, SciEx_217, SCR_012479, r3d100010243 | http://genome.cse.ucsc.edu https://doi.org/10.17616/R3RK5C |
SCR_005780 | The Human Genome Browser at UCSC, UCSC Genome Browser Group, University of California at Santa Cruz Genome Browser, UCSC Genome Bioinformatics | 2026-02-15 09:19:03 | 10026 | ||||||
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MIALAB - Medical Image Analysis Lab Resource Report Resource Website 10+ mentions |
MIALAB - Medical Image Analysis Lab (RRID:SCR_006089) | MIALAB | organization portal, data or information resource, laboratory portal, portal | MIALAB, headed by Dr. Vince Calhoun, focuses on developing and optimizing methods and software for quantitative analysis of structure and function in medical images with particular focus on the study of psychiatric illness. We work with many types of data, including functional magnetic resonance imaging (fMRI), diffusion tensor imaging (DTI), electroencephalography (EEG), structural imaging and genetic data. Much of our time is spent working on new methods for flexible analysis of brain imaging data. The use of data driven approaches is very useful for extracting potentially unpredictable patterns within these data. However such methods can be further improved by incorporating additional prior information as constraints, in order to benefit from what we know. To this end, we draw heavily from the areas of image processing, adaptive signal processing, estimation theory, neural networks, statistical signal processing, and pattern recognition. | software, data, data visualization, medical image, image, neuroimaging, fmri, diffusion tensor imaging, electroencephalography, structural imaging, genetic data, brain, image processing, adaptive signal processing, estimation theory, neural network, statistical signal processing, pattern recognition, mri |
has parent organization: Mind Research Network is parent organization of: Group ICA of fMRI Toolbox is parent organization of: Group ICA Of EEG Toolbox is parent organization of: MIALAB - Resting State Data |
Mental disease | nlx_151551 | SCR_006089 | Medical Image Analysis Lab, Medical Image Analysis Laboratory, MIA Laboratory, Medical Image Analysis (MIA) Laboratory | 2026-02-15 09:19:08 | 27 |
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