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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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DeepNeuro Resource Report Resource Website 1+ mentions |
DeepNeuro (RRID:SCR_016911) | software toolkit, software resource | Software Python package for neuroimaging data. Framework to design and train neural network architectures. Used in medical imaging community to ensure consistent performance of networks across variable users, institutions, and scanners. | Design and train neural network architectures, medical imaging, neuroimaging data, neuroimaging |
uses: Python Programming Language is related to: Massachusetts General Hospital has parent organization: Harvard University; Cambridge; United States |
NIDA T90 DA022759; NIDA R90 DA023427; NIH Blueprint for Neuroscience Research ; NIBI ; NIBIB T32 EB1680; NCI U01 CA154601; NCI U24 CA180927; NCI U24 CA180918; NIBIB P41 EB015896 |
PMID:32578020 | Free, Available for download, Freely available | SCR_016911 | 2026-08-09 09:07:07 | 2 | ||||||||
|
Scope Resource Report Resource Website 10+ mentions |
Scope (RRID:SCR_017454) | software application, software resource | Two photon microscope control software with multi area capabilities. | Two, photon, microscope, control, BRAIN Initiative | is recommended by: BRAIN Initiative | NINDS NS090475 | Free, Available for download, Freely available | SCR_017454 | 2026-08-09 09:07:20 | 15 | |||||||||
|
pyRayleighCuda Resource Report Resource Website |
pyRayleighCuda (RRID:SCR_017453) | software application, software resource | Python Rayleigh-Sommerfeld integral for acoustics with optional CUDA graphics processing unit (GPU) implementation. | Rayleigh-Sommerfeld, integral, acoustics, CUDA, graphics, processing, unit, BRAIN Initiative | is recommended by: BRAIN Initiative | NIMH MH109105 | Free, Freely available | SCR_017453 | 2026-08-09 09:07:04 | 0 | |||||||||
|
PyNWB Resource Report Resource Website 1+ mentions |
PyNWB (RRID:SCR_017452) | software application, software resource | Software Python package for working with Neurodata stored in Neurodata Without Borders files. Software providing API allowing users to read and create NWB formatted HDF5 files. Developed in support to NWB project with aim of spreading standardized data format for cellular based neurophysiology information. | Neurodata, stored, NWB, file, share, standardized, data, format, neurophysiology, BRAIN Initiative |
uses: Hierarchical Data Modeling Framework is used by: NWB Explorer is recommended by: BRAIN Initiative is listed by: OMICtools is listed by: Neurodata Without Borders is related to: Neurodata Extensions Catalog is related to: HDMF Common Schema is related to: NWB Inspector |
Kavli Foundation ; General Electric ; Howard Hughes Medical Institute ; Allen Institute for Brain Science ; NSF 0855272; International Neuroinformatics Coordinating Facility ; NIH BRAIN Initiative R24 MH116922 |
PMID:26590340 | Free, Available for downloading, Freely available | https://github.com/NeurodataWithoutBorders/pynwb | https://github.com/AllenInstitute/nwb-api | SCR_017452 | 2026-08-09 09:07:16 | 4 | ||||||
|
viridis Resource Report Resource Website 10+ mentions |
viridis (RRID:SCR_016696) | software toolkit, software resource | Software package which brings to R color scales. Created for the Python matplotlib library. | R, color, scale, Python, matplotlib, CRAN |
is affiliated with: R Project for Statistical Computing is affiliated with: CRAN |
Free, Available for download, Freely available | https://github.com/sjmgarnier/viridis | SCR_016696 | 2026-08-09 09:06:48 | 30 | |||||||||
|
nbdocker Resource Report Resource Website |
nbdocker (RRID:SCR_017159) | software application, software resource | Software tool as Jupyter Notebook extension for Docker. Each Docker container encapsulates its individual computing environment to allow different programming languages and computing environments to be included in one single notebook, provides user to document code as well as computing environment. | Jupyter, notebook, extension, docker, container, code, computing, environment, data | is related to: University of Washington; Seattle; USA | NHLBI U54 HL127624; NIGMS R01 GM126019; Institute of Technology at University of Washington Tacoma |
DOI:10.1101/309567 | Free, Available for download, Freely available | https://hub.docker.com/r/biodepot/nbdocker/ | SCR_017159 | 2026-08-09 09:06:58 | 0 | |||||||
|
EEGsynth Resource Report Resource Website 1+ mentions |
EEGsynth (RRID:SCR_018732) | software application, software resource | Open source Python codebase that provides real-time interface between open-hardware devices for electrophysiological recordings like EEG, EMG, and ECG, and analog and digital devices like MIDI, OSC, and analog synthesizers. This allows one to use electrical brain/body activity to flexibly control devices in real-time. | Codebase, electrophysiological recording, interface, analog, digital device, analog synthesizer, device control, electrical brain activity, EEG, EMG, ECG, BCI, Neurofeedback, Biofeedback, Music, MIDI, OSC, Python | Free, Freely available | https://www.eegsynth.org, http://pypi.org/project/eegsynth/ | SCR_018732 | 2026-08-09 09:07:17 | 2 | ||||||||||
|
paint.net Resource Report Resource Website 10+ mentions |
paint.net (RRID:SCR_017641) | software application, software resource | Software tool as image and photo editor for PCs that run Windows. Features user interface with support for layers, unlimited undo, special effects, and variety of useful and powerful tools. | Image, photo, editor | PMID:18941840 | Free, Available for download, Freely available | SCR_017641 | paint.net 4.2.8, Paint.NET | 2026-08-09 09:07:25 | 15 | |||||||||
|
kb_python Resource Report Resource Website 10+ mentions |
kb_python (RRID:SCR_018213) | software toolkit, software resource | Software Python package that wraps kallisto and bustools single-cell RNA-seq workflow. Used for single-cell RNA-seq pre-processing. Simplifies downloading and running of kallisto and bustools programs. Consists of kb ref and kb count commands. kb ref builds or downloads species specific index for pseudo alignment of reads and must be run prior to kb count and it runs kallisto index. kb count runs kallisto and bustools programs and is used for pre-processing of data from variety of single-cell RNA-seq technologies, and for number of different workflows (e.g. production of gene count matrices, RNA velocity analyses, etc.). | Wrapper, single cell RNA seq, pre-processing, species specific index, pseudo alignment, read, gene count matrice, RNA velocity analysis, data |
works with: kallisto works with: Bustools |
DOI:10.1038/nbt.3519 DOI:10.1101/673285 |
Free, Available for download, Freely available | SCR_018213 | 2026-08-09 09:07:30 | 18 | |||||||||
|
TreeBeST Resource Report Resource Website 50+ mentions |
TreeBeST (RRID:SCR_018173) | software toolkit, software resource | Software package to build, manipulate and display phylogenetic trees. Designed for building gene trees with known species tree and is highly efficient and accurate. | Phylogenetic tree, gene tree, phylogeny | Free, Available for download, Freely available | SCR_018173 | NJTREE, Tree Building guided by Species Tree | 2026-08-09 09:07:40 | 86 | ||||||||||
|
MendelIHT.jl Resource Report Resource Website 1+ mentions |
MendelIHT.jl (RRID:SCR_018292) | software application, software resource | Software Julia package that implements iterative hard thresholding as multiple regression model for GWAS. Built-in support for handling PLINK and VCF files, parallel computing, fits a variety of GLM models, and handles grouping/weighting SNPs. | GWAS, iterative hard thresholding, multiple regression, GLM model, feature selection, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: PLINK |
DOI:10.1101/697755 | Free, Available for download, Freely available | biotools:mendeliht.jl | https://bio.tools/mendeliht.jl | SCR_018292 | Mendel Iterative Hard Thresholding.jl, Mendel Iterative Hard Thresholding, MendelIHT | 2026-08-09 09:07:13 | 2 | ||||||
|
PhaseME Resource Report Resource Website 1+ mentions |
PhaseME (RRID:SCR_018739) | software toolkit, software resource | Software tool set to assess quality of per read phasing information and help to reduce errors during this process. | Variant Call Format Tools, quality assessment, read phasing, error, reduce error, read phasing information, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:phaseme | https://bio.tools/phaseme/ | SCR_018739 | 2026-08-09 09:07:39 | 1 | ||||||||
|
ACD/ChemSketch Resource Report Resource Website 10+ mentions |
ACD/ChemSketch (RRID:SCR_019272) | software application, software resource | Software tool as molecular structure drawing application by ACD Labs. Allows user to Draw chemical structures, reactions, and schema, and access variety of graphical tools and templates, Generate names from molecular structure and vice versa, Calculate molecular properties from chemical structure, Create professional reports, presentations, and publication ready figures, Communicate scientific information with clarity and ease. | Chemical structure, molecular structure, drawing application, generate molecular structure names, calculate molecular properties, create professional reports, ACD Labs | Restricted | SCR_019272 | ChemSketch | 2026-08-09 09:07:25 | 22 | ||||||||||
|
QuickFigures Resource Report Resource Website 1+ mentions |
QuickFigures (RRID:SCR_019082) | software toolkit, software resource | Software package to quickly transform microscope images into quality figures. User friendly tool for creating and formatting scientific figures, can export files into popular softwares like Adobe Illustrator, Microsoft Powerpoint, and Inkscape. | Transform microscope image, creating scientific figure, formatting scientific figure, quality fiqure | is a plug in for: ImageJ | DOI:10.1101/2020.09.24.311282 | SCR_019082 | 2026-08-09 09:07:21 | 1 | ||||||||||
|
American Optical: 860 Sliding Microtome Resource Report Resource Website 1+ mentions |
American Optical: 860 Sliding Microtome (RRID:SCR_018434) | instrument resource | THIS REOURCE IS NO LONGER IN SERVICE. Documented on September 29,2023. Sliding microtome used for cutting hard objects such as bone, wood, frozen celloidin, and paraffin preparations. Cutting thickness is adjustable from 1 to 40 microns. | Sliding Microtome, Instrument, Equipment, American Optical, USEDit, ABRF | is listed by: USEDit | THIS REOURCE IS NO LONGER IN SERVICE | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/main/PDF/SCR_018434.pdf | SCR_018451, SCR_019570 | https://rankinbiomed.com/wp-content/uploads/AO-860-Sliding-Microtome-Manual.pdf | SCR_018434 | 2026-08-09 09:07:42 | 1 | |||||||
|
dandi-cli Resource Report Resource Website 1+ mentions |
dandi-cli (RRID:SCR_019009) | software application, software resource | Command line client to facilitate common operations. | Command line client, facilite common operations, neurophysiology data integration, distributed archives, client | Free, Freely available | SCR_019009 | Distributed Archives for Neurophysiology Data Integration client, DANDI client | 2026-08-09 09:07:20 | 1 | ||||||||||
|
Conda Resource Report Resource Website 100+ mentions |
Conda (RRID:SCR_018317) | software toolkit, software resource | Software tool as cross platform, language agnostic binary package manager. Open source package management system and environment management system that runs on Windows, macOS and Linux. Can quickly install, run, and update packages and their dependencies. Package, dependency and environment management for any language—Python, R, Ruby, Lua, Scala, Java, JavaScript, C/ C++, FORTRAN, and more. Created for Python programs, but it can package and distribute software for any language. Conda can be combined with continuous integration systems such as Travis CI and AppVeyor to provide frequent, automated testing of your code. Conda package and environment manager is included in all versions of Anaconda and Miniconda. | Package manager system, environment management system, software distribution, integration system, automated code testing |
is related to: BioConda is related to: RNAProt |
Free, Available for download, Freely available | https://conda.io/, https://github.com/conda/conda | SCR_018317 | 2026-08-09 09:07:41 | 116 | |||||||||
|
BioConda Resource Report Resource Website 50+ mentions |
BioConda (RRID:SCR_018316) | software application, software resource | Software distribution management for life sciences. Channel for Conda package manager specializing in bioinformatics software. Consists of repository of recipes hosted on GitHub, build system turning these recipes into conda packages, repository of packages containing bioinformatics packages ready to use with conda install. | Software distribution management, bioinformatic software, package repository, GitHub, conda, bio.tools |
lists: CCS is listed by: bio.tools is listed by: Debian is related to: Conda is related to: RNAProt |
Intramural Program of the National Institute of Diabetes and Digestive and Kidney Diseases ; Netherlands Organisation for Scientific Research ; German Research Foundation ; NYU Abu Dhabi Research Institute |
PMID:29967506 | Free, Available for download, Freely available | biotools:bioconda | https://bio.tools/bioconda | SCR_018316 | Bioconda | 2026-08-09 09:07:13 | 73 | |||||
|
cvequality Resource Report Resource Website 1+ mentions |
cvequality (RRID:SCR_019124) | software toolkit, software resource | Software R package contains functions to test for significant differences in coefficients of variation among multiple groups of observations. | testing significant differences, coefficients of variation, multiple groups | is listed by: CRAN | Free, Available for download, Freely available | https://CRAN.R-project.org/package=cvequality | SCR_019124 | 2026-08-09 09:07:22 | 2 | |||||||||
|
GWAS Quality Control Pipeline Resource Report Resource Website 1+ mentions |
GWAS Quality Control Pipeline (RRID:SCR_019241) | software toolkit, software resource | Software tool as scalable GWAS Quality Control pipeline for biobank scale datasets. | GWAS, data quality control, biobank scale datasets, genome wide association study | is related to: GWASdb | Free, Available for download, Freely available | SCR_019241 | BIGwas QC | 2026-08-09 09:07:50 | 4 |
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