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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Group Sparse Canonical Correlation Analysis Resource Report Resource Website |
Group Sparse Canonical Correlation Analysis (RRID:SCR_014977) | GSCCA | data analysis software, data processing software, software application, software resource | Group Sparse Canonical Correlation Analysis is a method designed to study the mutual relationship between two different types of data. | group analysis, correlation analysis | has parent organization: NeuroImaging Tools and Resources Collaboratory (NITRC) | NSF ; NIH |
Available for download | SCR_014977 | SciCrunch Registry | 2026-10-17 01:28:58 | 0 | ||||||||
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HISAT2 Resource Report Resource Website 10000+ mentions |
HISAT2 (RRID:SCR_015530) | data analysis software, data processing software, sequence analysis software, software application, software resource, source code | Graph-based alignment of next generation sequencing reads to a population of genomes. | alignment program, mapping reads, population genomics, human genome, bio.tools |
is used by: Fcirc is listed by: Debian is listed by: bio.tools is related to: TopHat has parent organization: Johns Hopkins University; Maryland; USA is required by: SL-quant is hosted by: GitHub |
NLM R01-LM06845; NIGMS R01-GM083873; NSF CCF-0347992 |
PMID:25751142 DOI:10.1038/s41587-019-0201-4 |
Available for download | OMICS_07225, biotools:hisat2 | https://github.com/infphilo/hisat2, https://bio.tools/hisat2, https://sources.debian.org/src/hisat2/ | SCR_015530 | SciCrunch Registry | HISAT | 2026-10-17 01:29:12 | 20753 | |||||
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BECA Resource Report Resource Website 1+ mentions |
BECA (RRID:SCR_015846) | BECA | data processing software, data visualization software, image analysis software, software application, software resource | Visualization and analysis software for interactive visual exploration and mining of fiber-tracts and brain networks with their genetic determinants and functional outcomes. BECA includes an fMRI and Diseases Analysis version as well as a Genome Explorer version. | visual exploration, brain, neuroscience, network, genetic determinant, fmri, neuroimaging, genome | has parent organization: Indiana University School of Medicine; Indiana; USA | NIA P30 AG10133; NIA R01 AG19771; NIA RC2 AG036535; NIA U01 AG024904; NIBIB R01 EB022574; NLM R01 LM011360; NSF IIS-1117335 |
PMID:27171688 | Free, Available for download | SCR_015846 | SciCrunch Registry | Brain Explorer for Connectome Analysis (BECA), BECA - Brain Explorer for Connectome Analysis | 2026-10-17 01:29:05 | 5 | ||||||
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Avogadro Resource Report Resource Website 1000+ mentions |
Avogadro (RRID:SCR_015983) | data analysis software, data processing software, data visualization software, software application, software resource, software toolkit | Software for semantic chemical editing, visualization, and analysis. It is designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. | semantic, optimization, crystallography, chemical, editor, visualization, analysis, molecular, modeling, drug, design, biomolecule, simulation, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
Engineering Research Development Center W912HZ-11-P-0019; NSF DMR-1005413 |
PMID:22889332 DOI:10.1186/1758-2946-4-17 |
Open source, Free, Free to download | OMICS_04967, biotools:avogadro | http://avogadro.openmolecules.net/, https://github.com/avogadro, https://bio.tools/avogadro, https://sources.debian.org/src/axe-demultiplexer/ | SCR_015983 | SciCrunch Registry | 2026-10-17 01:29:19 | 2237 | ||||||
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Linear Fascicle Evaluation Resource Report Resource Website 1+ mentions |
Linear Fascicle Evaluation (RRID:SCR_016153) | data analysis software, data processing software, software application, software resource | 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 | Indiana University Areas of Emergent Research initiative Learning: Brains ; Machines ; Children ; NCATS ULT TR001108; NSF BCS-1734853; NSF IIS-1636893 |
Free, Available for download, Demo available | SCR_016153 | SciCrunch Registry | 2026-10-17 01:29:22 | 1 | |||||||||
|
HyPhy Resource Report Resource Website 1000+ mentions |
HyPhy (RRID:SCR_016162) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | 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 |
NIGMS R01 ; NIH R01 AI47745; NIH U01 AI43638; NSF DBI-0096033; NSF DEB-9996118; 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 |
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 | SciCrunch Registry | HyPhy:Hypothesis Testing using Phylogenies, Hyphy-pt | 2026-10-17 01:29:22 | 1586 | |||||
|
Mapping Population-based Structural Connectomes Resource Report Resource Website |
Mapping Population-based Structural Connectomes (RRID:SCR_016232) | data analysis software, data processing software, software application, software resource | 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 | CPRIT RR150054; NIMH MH086633; NIMH MH092335; NSF DMS-1407655; NSF DMS1127914; NSF SES-1357666 |
Free for non-commercial use, Available for download | SCR_016232 | SciCrunch Registry | 2026-10-17 01:29:23 | 0 | ||||||||||
|
Brain Imaging Data Structure (BIDs) Resource Report Resource Website 100+ mentions |
Brain Imaging Data Structure (BIDs) (RRID:SCR_016124) | BIDS | data or information resource, narrative resource, portal, standard specification | Standard specification for organizing and describing outputs of neuroimaging experiments. Used to organize and describe neuroimaging and behavioral data by neuroscientific community as standard to organize and share data. BIDS prescribes file naming conventions and folder structure to store data in set of already existing file formats. Provides standardized templates to store associated metadata in form of Javascript Object Notation (JSON) and tab-separated value (TSV) files. Facilitates data sharing, metadata querying, and enables automatic data analysis pipelines. System to curate, aggregate, and annotate neuroimaging databases. Intended for magnetic resonance imaging data, magnetoencephalography data, electroencephalography data, and intracranial encephalography data. | Data storing structure, neuroimaging, standardized template, data sharing, MRI data, MEG data, EEG data, iEEG data, FASEB list |
is used by: OpenNeuro is used by: SPARC Portal is used by: SPARC Data Standard is listed by: FAIRsharing is related to: BIDS-Matlab is related to: NiPoppy works with: MNE-BIDS |
European Regional Development Fund ; German federal state of Sachsen-Anhalt ; International Neuroinformatics Coordinating Facility ; Laura and John Arnold Foundation ; Medical Research Council United Kingdom ; NIAAA U01 AA021697; NIGMS P20 GM103472; NIMH Intramural Research Program ; NSF 1429999; Wellcome Trust |
PMID:27326542 PMID:29917016 PMID:31239435 PMID:31239438 PMID:37744469 |
Free, Freely available | https://bids-specification.readthedocs.io/en/stable/, https://doi.org/10.25504/FAIRsharing.rd1j6t | SCR_016124 | SciCrunch Registry | Brain Imaging Data Structure, BIDS, Brain Imaging Data Structure (BIDS), Brain Imaging Data Structure v1.4.0 | 2026-10-17 01:29:21 | 235 | |||||
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nelpy Resource Report Resource Website 1+ mentions |
nelpy (RRID:SCR_016209) | data analysis software, data processing software, data visualization software, software application, software resource, software toolkit | Software toolkit for neuroelectrophysiology object modeling and data analysis in Python. Open source Python package for analysis of neuroelectrophysiology data. | model, modelling, python, neuroelectrophysiology, object, neuroimaging, analysis, neurophysiology, electrophysiology, BRAIN Initiative | is recommended by: BRAIN Initiative | Human Frontiers Science Program RGY0088; NSF CBET-1351692; NSF IOS-1550994 |
Free, Available for download, Freely available | SCR_016209 | SciCrunch Registry | Nelpy (Neuroelectrophysiology) | 2026-10-17 01:29:04 | 3 | ||||||||
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IHM-dictionary Resource Report Resource Website 1+ mentions |
IHM-dictionary (RRID:SCR_016186) | software resource | Software resource for a data representation for integrative/hybrid methods of modeling macromolecular structures. | macromolecule, mmcif, pdb, protein, database, databank, spectroscopy, microscopy, crystallography, proteomic | is related to: PDB-Dev | NSF DBI-1519158 | Free, Available for download | SCR_016186 | SciCrunch Registry | 2026-10-17 01:29:04 | 4 | |||||||||
|
PDB-Dev Resource Report Resource Website 10+ mentions |
PDB-Dev (RRID:SCR_016185) | data repository, service resource, storage service resource | Data repository for integrative/hybrid structural models of macromolecules and their assemblies. This includes atomistic models as well as multi-scale models consisting of different coarse-grained representations. | protein, prototype, deposition, integration, hybrid, model, macromolecule, assembly, crystallography, spectroscopy, microscopy, |
is related to: IHM-dictionary has parent organization: Worldwide Protein Data Bank (wwPDB) has parent organization: Rutgers University; New Jersey; USA |
NSF DBI-1519158 | Account required, Freely available, The research community can contribute to this resource | SCR_016185 | SciCrunch Registry | 2026-10-17 01:29:09 | 36 | |||||||||
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Centrifuge Classifier Resource Report Resource Website 10+ mentions |
Centrifuge Classifier (RRID:SCR_016665) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software for rapid and sensitive classification of metagenomic sequences. Used for the classification of DNA sequences from microbial samples and analysis of large metagenomics data sets on conventional desktop computers. | classification, large, metagenomic, sequence, DNA, microbial, sample, analysis, data, desktop, computer, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is related to: Pavian has parent organization: Center for Computational Biology at JHU |
NHGRI R01 HG006677; NIGMS R01 GM083873; NSF ABI1356078; U. S. Army Research Office W911NF1410490 |
DOI:10.1101/gr.210641.116 | Free, Available for download, Freely available | biotools:centrifuge, OMICS_12217 | https://github.com/infphilo/centrifuge, https://bio.tools/centrifuge, https://sources.debian.org/src/centrifuge/ | SCR_016665 | SciCrunch Registry | 2026-10-17 01:29:16 | 10 | ||||||
|
Libra Resource Report Resource Website |
Libra (RRID:SCR_016608) | data analysis software, data analytics software, data processing software, sequence analysis software, software application, software resource | Hadoop based tool for massive comparative metagenomics analysis. Compute the similarity between metagenomic samples. | gene, distance, matrix, computation, k-mer-based, sequence, comparison, Hadoop, metagenomic, sample, bio.tools |
is listed by: bio.tools is listed by: Debian |
NSF 1640775 | Free, Available for download, Freely available | biotools:Libra_k-mer | https://bio.tools/Libra_k-mer | SCR_016608 | SciCrunch Registry | 2026-10-17 01:29:15 | 0 | |||||||
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TopDom Resource Report Resource Website 10+ mentions |
TopDom (RRID:SCR_016964) | TOPDOM | data analysis software, data processing software, software application, software resource, software toolkit | Software tool to identify Topological Domains, which are basic builiding blocks of genome structure. Detects topological domains in a linear time., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | identify, topological, domain, genome, structure, linear, time, data, analysis |
has parent organization: University of Southern California; Los Angeles; USA works with: CCTOP |
Arnold and Mabel Beckman foundation ; NHLBI U01 HL108634; NIDDK U54 DK107981; NSF CAREER 0747475; NSF CAREER 1150287; Pew Charitable Trusts |
PMID:26704975 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016964 | SciCrunch Registry | TOPological DOMains, Topological Domains, TopDom_v0.0.2, TopDom_v0.0.1 | 2026-10-17 01:29:20 | 11 | ||||||
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PICRUSt Resource Report Resource Website 10+ mentions |
PICRUSt (RRID:SCR_016855) | PICRUSt | simulation software, software application, software resource | Software package to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. Used to predict which gene families are present and then combines gene families to estimate the composite metagenome. | predict, metagenome, functional, content, DNA, sample, marker, gene, sequence, data, microbiome, 16S, RNA | is related to: PICRUSt2 | ARO W911NF1110473; Canada Research Chairs program ; Canadian Institutes of Health Research ; Crohn’s and Colitis Foundation of America ; Howard Hughes Medical Institute ; NHGRI R01 HG004872; NHGRI R01 HG005969; NHGRI U01 HG004866; NIDDK P01 DK078669; NSF CAREER DBI1053486; Sloan Foundation |
PMID:23975157 | Free, Available for download, Freely available | SCR_016856 | SCR_016855 | SciCrunch Registry | Phylogenetic Investigation of Communities by Reconstruction of Unobserved States, PICRUSt | 2026-10-17 01:29:18 | 45 | |||||
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BinPacker Resource Report Resource Website 10+ mentions |
BinPacker (RRID:SCR_017038) | data analysis software, data processing software, software application, software resource | Software tool as de novo trascriptome assembler for RNA-Seq data. Used to assemble full length transcripts by remodeling problem as tracking set of trajectories of items over splicing graph. Input RNA-Seq reads in fasta or fastq format, and ouput all assembled candidate transcripts in fasta format. Operating system Unix/Linux. | de novo, transcriptome, assembler, RNAseq, data, full, length, transcript, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
National Natural Science Foundation of China ; NCRR P20 RR01 6460; NIGMS P20 GM103429; NSF 1553680 |
PMID:26894997 | Free, Available for download, Freely available | OMICS_11199, biotools:binpacker | http://sourceforge.net/projects/transcriptomeassembly/files/BinPacker_1.0.tar.gz/download, http://sourceforge.net/projects/transcriptomeassembly/files/BinPacker_binary.tar.gz/download, https://bio.tools/binpacker | SCR_017038 | SciCrunch Registry | 2026-10-17 01:29:12 | 10 | ||||||
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Microfluidic device to attain high spatial and temporal control of oxygen Resource Report Resource Website |
Microfluidic device to attain high spatial and temporal control of oxygen (RRID:SCR_017131) | instrument resource | Device to control spatial and temporal variations in oxygen tensions to better replicate in vivo biology. Consists of three parallel connected tissue chambers and oxygen scavenger channel placed adjacent to these tissue chambers. Provides consistent control of spatial and temporal oxygen gradients in tissue microenvironment and can be used to investigate important oxygen dependent biological processes present in cancer, ischemic heart disease, and wound healing. | device, instrument, control, spatial, temporal, variation, oxygen, tension, tissue, microenvironment | NCATS UH3 TR00048; NCI R01 CA170879; NIDDK UC4 DK104202; NSF DGE-1143954 |
PMID:30571786 | SCR_017131 | SciCrunch Registry | 2026-10-17 01:29:15 | 0 | ||||||||||
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Seizure-Waves Resource Report Resource Website |
Seizure-Waves (RRID:SCR_017455) | data analysis software, data processing software, software application, software resource | Analysis and modeling code for waves of seizure activity. | Analysis, modeling, wave, seizure, brain, activity, BRAIN Initiative | is recommended by: BRAIN Initiative | NSF 1451384 | Free, Freely available | SCR_017455 | SciCrunch Registry | SeizureWaves, Seizure Waves, Seizure-Waves | 2026-10-17 01:29:17 | 0 | ||||||||
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cytoNet Resource Report Resource Website |
cytoNet (RRID:SCR_017465) | analysis service resource, data processing software, image analysis software, production service resource, service resource, software application, software resource | Cloud based analysis software for cell population microscopy images. Network Analysis of Cell Communities cytoNet image analysis software designed to quantify structure of cell communities from microscope images, using principles of graph theory. | Cell, population, microscopy, image, network, analysis, quantify, structure, BRAIN Initiative | is recommended by: BRAIN Initiative | NSF 1533708 | Free, Freely available | SCR_017465 | SciCrunch Registry | 2026-10-17 01:29:47 | 0 | |||||||||
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Fusion ICA Toolbox Resource Report Resource Website 10+ mentions |
Fusion ICA Toolbox (RRID:SCR_003494) | FIT | data processing software, software application, software resource, software toolkit | A MATLAB toolbox which implements the joint Independent Component Analysis (ICA), parallel ICA and CCA with joint ICA methods. It is used to to extract the shared information across modalities like fMRI, EEG, sMRI and SNP data. * Environment: Win32 (MS Windows), Gnome, KDE * Operating System: MacOS, Windows, Linux * Programming Language: MATLAB * Supported Data Format: ANALYZE, NIfTI-1 | analysis, functional magnetic resonance imaging, cca, image, eeg, neuroimaging, matlab, smri, snp, mri, algorithm, reusable library, independent component analysis, principal component analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps has parent organization: University of New Mexico; New Mexico; USA |
NIBIB 1RO1EB005846; NSF 0612076 |
GNU General Public License | nif-0000-36743 | http://www.nitrc.org/projects/fit | SCR_003494 | SciCrunch Registry | Fusion ICA Toolbox (FIT) | 2026-10-17 01:32:14 | 13 |
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