Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Linear Fascicle Evaluation Resource Report Resource Website 1+ mentions |
Linear Fascicle Evaluation (RRID:SCR_016153) | software resource, software application, data analysis software, data processing software | Software that implements a framework to encode structural brain connectomes into multidimensional arrays (tensors). Encoding Connectomes provides an agile framework for computing over connectome edges and nodes. | connectome, encode, framework, neuroanatomy, tract, dissection, array, tensor, edge, node | requires: MATLAB | NSF IIS-1636893; NSF BCS-1734853; NCATS ULT TR001108; Indiana University Areas of Emergent Research initiative Learning: Brains ; Machines ; Children |
Free, Available for download, Demo available | SCR_016153 | 2026-08-08 12:00:49 | 1 | |||||||||
|
AMBER Resource Report Resource Website 1000+ mentions |
AMBER (RRID:SCR_016151) | AMBER | software toolkit, software resource, software application, data analysis software, data visualization software, data processing software | Software toolkit for the comparative assessment of genome reconstructions from metagenome benchmark datasets. It provides performance metrics, results rankings, and comparative visualizations for assessing multiple programs or parameter effects. | binning, metagenomics, benchmarking, biobox, evaluation, comparison, reconstruction, metric, |
is used by: CHARMM-GUI is listed by: SoftCite |
DOI:10.1101/239582 | Free, Available for download | SCR_016151 | AMBER: Assessment of Metagenome BinnERs | 2026-08-08 12:00:50 | 2205 | |||||||
|
NeMOarchive Resource Report Resource Website 100+ mentions |
NeMOarchive (RRID:SCR_016152) | NeMO | data or information resource, database, service resource, storage 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 | 2026-08-08 12:00:29 | 126 | ||||||
|
HIRN Consortium on Targeting and Regeneration Resource Report Resource Website |
HIRN Consortium on Targeting and Regeneration (RRID:SCR_016201) | HIRN-CTAR, CTAR, CTR, HIRN-CTR | data or information resource, portal, organization portal, consortium | Consortium that is an independent research initiative of the Human Research Information Network (HIRN). It is investigating methods to increase or maintain functional beta cell mass in T1D through targeted manipulation of islet plasticity or engineered protection of beta cells from immune-mediated destruction. | plasticity, bioengineering, cell, beta, cell, death | is organization facet of: Human Islet Research Network (HIRN) | NIDDK ; NIDDK U01 DK104162; NIDDK UC4 DK104211; NIDDK UC4 DK104204; NIDDK UC4 DK104209; NIDDK UC4 DK104143; NIDDK UC4 DK104119; NIDDK UC4 DK116241; NIDDK UC4 DK116264; NIDDK UC4 DK116252; NIDDK UC4 DK116255; NIDDK UC4 DK116280 |
SCR_016201 | Consortium on Targeting and Regeneration (HIRN-CTAR) | 2026-08-08 12:00:50 | 0 | ||||||||
|
HyPhy Resource Report Resource Website 1000+ mentions |
HyPhy (RRID:SCR_016162) | sequence analysis software, software toolkit, software resource, software application, data analysis software, data processing software | 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 | 2026-08-08 12:00:50 | 1586 | |||||
|
Indelible Resource Report Resource Website 10+ mentions |
Indelible (RRID:SCR_016163) | software resource, software application, simulation software | Software that generates nucleotide, amino acid and codon sequence data by simulating insertions and deletions (indels) as well as substitutions. It is used for biological sequence simulation of multi-partitioned nucleotide, amino-acid, or codon data sets through the processes of insertion, deletion, and substitution in continuous time. | indel, insertion, deletion, biological, sequence, simulation, multi-partitioned, nucleotide, amio-acid, codon, data, set, insertion, deletion, substitution, continous, time, non-homogeneous, non-stationary, phylogeny, simulator, evolution |
is listed by: Debian is listed by: OMICtools |
EPSRC/MRC Doctoral Training Centre studentship ; BBSRC |
PMID:19423664 | Free, Available for download | OMICS_15369 | https://sources.debian.org/src/indelible/ | SCR_016163 | 2026-08-08 12:00:29 | 24 | ||||||
|
zUMIs Resource Report Resource Website 100+ mentions |
zUMIs (RRID:SCR_016139) | software resource, software application, data analysis software, data processing software | Software pipeline to process RNA-seq data with UMIs. The input to this pipeline is paired-end fastq files, where one read contains the cDNA sequence and the other read contains UMI and Cell Barcode information. | single-cell, RNA-seq, UMI, Genomics, shell, r, perl, rna, cdna, cell, sequencing, bio.tools |
is listed by: bio.tools is listed by: Debian |
DOI:10.1101/153940 | Open source, Free, Available for download | biotools:zumis | https://bio.tools/zumis | SCR_016139 | zumi | 2026-08-08 12:00:49 | 128 | ||||||
|
Microsoft Excel Resource Report Resource Website 10000+ mentions |
Microsoft Excel (RRID:SCR_016137) | software resource, software application, data analysis software, data visualization software, data processing 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 | 2026-08-08 12:00:49 | 90742 | ||||||||
|
Fastml Resource Report Resource Website 100+ mentions |
Fastml (RRID:SCR_016092) | web application, software resource, data access protocol, web service | Web application for the reconstruction of ancestral sequences. It computes maximum likelihood ancestral sequence reconstruction based on the phylogenetic relations between homologous sequences. | ancestral, amino-acid, sequence, reconstruction, phylogenetic, relation, accurate, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
Israel Science Foundation 878/09; Bioinformatics Center at Tel-Aviv University |
PMID:22661579 | Free, Freely available | biotools:fastml, OMICS_08650 | https://bio.tools/fastml, https://sources.debian.org/src/fastml/ | SCR_016092 | The FastML Server | 2026-08-08 12:00:48 | 111 | |||||
|
Gubbins Resource Report Resource Website 500+ mentions |
Gubbins (RRID:SCR_016131) | sequence analysis software, software resource, software application, data analysis software, data processing software | Software application as an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. It is used for phylogenetic analysis of genome sequences and generating highly accurate reconstructions under realistic models of short-term bacterial evolution., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | rapid, phylogenetic, analysis, large, sample, recombinant, bacteria, whole, genome, sequence, loci, elevated, densities, base, substitiution, mutatiion, outside, region, evolution, alignment |
is listed by: Debian is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust 098051 | PMID:25414349 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_14386 | https://sources.debian.org/src/gubbins/ | SCR_016131 | Gubbins: Genealogies Unbiased By recomBinations In Nucleotide Sequences | 2026-08-08 12:00:49 | 604 | |||||
|
MediBeacon Studio Software Resource Report Resource Website |
MediBeacon Studio Software (RRID:SCR_016252) | software resource, software application, data analysis software, data processing software | Software used to analyze glomerular filtration rate (GFR) measurement from MediBeacon GFR monitor. It is used with the Transdermal Continuous Renal Function Monitor. | nephrology, renal, kidney, gfr, glomerulus, transdermal, skin, measurement | has parent organization: MediBeacon | Commercially available, Comes with device purchase | SCR_016252 | Studio Software, MediBeacon Software, Preclinical Data Studio | 2026-08-08 12:00:29 | 0 | |||||||||
|
SciScore Resource Report Resource Website 10+ mentions |
SciScore (RRID:SCR_016251) | web application, text-mining software, software resource, software application | Text-mining software that reviews methods sections of scientific articles. It provides a numerical score to represent the "reproducibility" of the article's research. | mine, text, method, journal, paper, article, research, science, biomedicine, neuroscience, scicrunch, nif, ASWG | is related to: SciCrunch | PMID:35759334 PMID:33196023 |
Used by SciCrunch, Freely available, Available to the research community | http://sci-score.com | SCR_016251 | Sci Score, SciCrunch SciScore | 2026-08-08 12:00:51 | 13 | |||||||
|
GraPhlAn Resource Report Resource Website 100+ mentions |
GraPhlAn (RRID:SCR_016130) | software resource, software application, data visualization software, data processing software | Software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. Used for concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation as a high-resolution microbial tree of life with taxonomic annotations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | circular, high, resolution, microbal, tree, taxonomy, annotation, phylogenetic, investigation |
is listed by: Debian is listed by: OMICtools has parent organization: Harvard University; Cambridge; United States |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_11549 | https://huttenhower.sph.harvard.edu/graphlan, https://sources.debian.org/src/graphlan/ | SCR_016130 | Graphlan | 2026-08-08 12:00:49 | 186 | |||||||
|
BioPlex Resource Report Resource Website 1000+ mentions |
BioPlex (RRID:SCR_016144) | data or information resource, database, service resource, storage service resource, data repository | Database of cell lines with each expressing a tagged version of a protein from the ORFeome collection. The overarching project goal is to determine protein interactions for every member of the collection. | cell, line, protein, immunopurification, mass, spectrometry, interaction, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: Harvard Medical School; Massachusetts; USA |
NHGRI U41HG006673; NIDDK K01 DK098285; Canadian Institutes for Health Research |
PMID:28514442 | biotools:bioplex_2.0 | https://bio.tools/bioplex_2.0 | SCR_016144 | BioPlex (biophysical interactions of ORFeome-based complexes), Harvard BioPlex, Biophysical Interactions of Orfeome-based comPLEXes (BioPLEX) | 2026-08-08 12:00:29 | 1378 | ||||||
|
mentha Resource Report Resource Website 100+ mentions |
mentha (RRID:SCR_016148) | web application, data or information resource, software resource, software application, database, data analysis software, data processing software | Software that archives evidence collected from different sources, then analyzes and presents these data. Its data come from manually curated protein-protein interaction databases that have adhered to the IMEx consortium. | protein, ppi, imex, interactome, archival, bio.tools, FASEB list |
uses: PSICQUIC Registry is listed by: Debian is listed by: bio.tools is related to: IMEx - The International Molecular Exchange Consortium |
PMID:23900247 | biotools:mentha, r3d100011124 | https://bio.tools/mentha, https://doi.org/10.17616/R3SP8V | SCR_016148 | 2026-08-08 12:00:29 | 156 | ||||||||
|
Mass Univariate ERP Toolbox Resource Report Resource Website 1+ mentions |
Mass Univariate ERP Toolbox (RRID:SCR_016108) | software resource, software application, data analysis software, data visualization software, data processing software | Software toolkit of Matlab functions for analyzing and visualizing large numbers of t-tests performed on event-related potential data. The toolbox supports within-subject and between-subject t-tests with false discovery rate controls and control of the family-wise error rate via permutation tests. | matlab, analysis, t test, statistic, erp, event related potential, visualization, neuroimaging, erf, magnetic, resonance, imaging | requires: MATLAB | NICHD HD22614; NIA AG08313 |
PMID:21895683 | Free, Available for download | https://openwetware.org/wiki/Mass_Univariate_ERP_Toolbox | SCR_016108 | 2026-08-08 12:00:49 | 6 | |||||||
|
iELVis Resource Report Resource Website 10+ mentions |
iELVis (RRID:SCR_016109) | software resource, software application, data visualization software, data processing software | Software toolkit consisting of MATLAB and Bash scripts for intracranial electrode localization/visualization. It maps electrodes to various anatomical and functional atlases, and overlays electrode data over functional neuroimaging data. Software for intracranial electrode localization and visualization. | electrode, stimulus, visualization, brain, neuroimaging, intracranial, localization, anatomy, functional, BRAIN Initiative | is recommended by: BRAIN Initiative | Swiss National Science Foundation PBGEP3_139829; Swiss National Science Foundation P300P3_148388; Natural Sciences and Engineering Research Council of Canada RGPIN-2014-04465; Page and Otto Marx Jr. Foundation |
PMID:28192130 | Open source, Free, Available for download | https://github.com/iELVis/iELVis | SCR_016109 | iELVis (intracranial electrode visualization), Intracranial ELectrode VISualization | 2026-08-08 12:00:28 | 47 | ||||||
|
HIRN Consortium on Human Islet Biomimetics Resource Report Resource Website |
HIRN Consortium on Human Islet Biomimetics (RRID:SCR_016199) | HIRN-CHIB, CHIB | data or information resource, portal, organization portal, consortium | Consortium that is an independent research initiative of the Human Research Information Network (HIRN). It is combining advances in beta cell biology and cell biology with tissue engineering technologies to develop microdevices that support functional human islets. | beta, cell, biology, tissue, bioengineering, nanoengineering, human, stem | is organization facet of: Human Islet Research Network (HIRN) | NIDDK ; NIDDK U01 DK104162; NIDDK UC4 DK104208; NIDDK UC4 DK104196; NIDDK UC4 DK104202; NIDDK UC4 DK104165; NIDDK UC4 DK116283 |
SCR_016199 | Consortium on Human Islet Biomimetics (HIRN-CHIB) | 2026-08-08 12:00:50 | 0 | ||||||||
|
Mapping Population-based Structural Connectomes Resource Report Resource Website |
Mapping Population-based Structural Connectomes (RRID:SCR_016232) | software resource, software application, data analysis software, data processing software | Data analysis software that can simultaneously characterize a large number of white matter bundles within and across different subjects for group analysis. It has three major components: construction of the structural connectome for the whole brain, low-dimensional representation of streamlines in each connection, and multi-level connectome analysis. | dwi, t1, tractography, algorithm, white matter, bundle, gray matter, shape, analysis, network, workflow | NIMH MH086633; NIMH MH092335; NSF SES-1357666; NSF DMS-1407655; CPRIT RR150054; NSF DMS1127914 |
Free for non-commercial use, Available for download | SCR_016232 | 2026-08-08 12:00:51 | 0 | ||||||||||
|
Garlic Resource Report Resource Website 10+ mentions |
Garlic (RRID:SCR_016118) | sequence analysis software, software resource, software application, data analysis software, data visualization software, data processing software | Software application for visualization and editing of biomolecules. Used for the investigation of membrane proteins, visualization of other proteins and geometric objects, and analysis of protein sequences. | visualization, editing, biomolecule, investigation, membrane, protein, analyze, sequence |
is listed by: Debian is listed by: OMICtools |
Open source, Free, Available for download | OMICS_21303 | https://sources.debian.org/src/garlic/ | SCR_016118 | 2026-08-08 12:00:48 | 38 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the kravitz2 Resources search. From here you can search through a compilation of resources used by kravitz2 and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that kravitz2 has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on kravitz2 then you can log in from here to get additional features in kravitz2 such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into kravitz2 you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
Data set from Kravitz, Owen and Kretizer's 2012 paper "Optogenetic identification of striatal projection neuron subtypes during in vivo recordings."
