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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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karyoploteR Resource Report Resource Website 10+ mentions |
karyoploteR (RRID:SCR_021824) | software toolkit, software resource | Software R package used to karyoplots. Bioconductor package to plot customizable genomes displaying arbitrary data. | Plot arbitrary data along genome, plot data, arbitrary data, customizable genomes | Spanish Ministry of Science and Innovation ; Government of Catalonia ; Spanish Association Against Cancer |
PMID:28575171 | Free, Available for download, Freely available | https://github.com/bernatgel/karyoploteR | SCR_021824 | 2026-08-09 09:07:43 | 21 | ||||||||
|
qudi-HiM Resource Report Resource Website 1+ mentions |
qudi-HiM (RRID:SCR_022114) | software toolkit, software resource | Software package for control of optical microscope setups with different hardware components optimized to perform multiplexed imaging experiments. Modular laboratory experiment management suite. | control of optical microscope setups, multiplexed imaging experiments | Free, Available for download, Freely available | SCR_022114 | 2026-08-09 09:08:10 | 3 | |||||||||||
|
CellChat Resource Report Resource Website 500+ mentions |
CellChat (RRID:SCR_021946) | software toolkit, software resource | Software R toolkit for inference, visualization and analysis of cell-cell communication from single cell data.Quantitatively infers and analyzes intercellular communication networks from single-cell RNA-sequencing data. Predicts major signaling inputs and outputs for cells and how those cells and signals coordinate for functions using network analysis and pattern recognition approaches. Classifies signaling pathways and delineates conserved and context specific pathways across different datasets. | inference, visualization, analysis, cell-cell communication, single cell data, intercellular communication networks, single-cell RNA-sequencing data | NSF DMS1763272; Simons Foundation ; NIH U01 AR073159; NIGMS R01 GM123731; NIH P30 AR07504; Pew Charitable Trust ; LEO Foundation ; UC Irvine ; Howard Hughes Medical Institute |
PMID:33597522 | Free, Available for download, Freely available | http://www.cellchat.org/ | SCR_021946 | 2026-08-09 09:08:18 | 753 | ||||||||
|
MeshParty Resource Report Resource Website 1+ mentions |
MeshParty (RRID:SCR_021873) | software toolkit, software resource | Software package for working with neuronal meshes, skeletons, and annotations from electron microscopy data. Used to work with meshes, designed around use cases for analyzing neuronal morphology. | neuronal meshes, skeletons, annotations, electron microscopy data, analyzing neuronal morphology | Free, Available for download, Freely available | SCR_021873 | 2026-08-09 09:08:18 | 4 | |||||||||||
|
endoR Resource Report Resource Website 1+ mentions |
endoR (RRID:SCR_021916) | software toolkit, software resource | Software R package to interpret fitted tree ensemble model.Used to extract and visualize how predictive variables contribute to tree ensemble model accuracy. | Fitted tree ensemble model interpretation, decision ensemble, tree ensemble model accuracy, predictive variables, pairwise interactions, straightforward interpretation network | DOI:10.1101/2022.01.03.474763 | Free, Available for download, Freely available | SCR_021916 | 2026-08-09 09:08:07 | 1 | ||||||||||
|
AutoPilot Resource Report Resource Website 1+ mentions |
AutoPilot (RRID:SCR_021518) | software toolkit, software resource | Software tool as open source Python framework for behavioral neuroscience that distributes experiments over networked swarms of Raspberry Pis. Toolkit of flexible modules to design experiments without rigid programming and API limitations. | Running behavioral experiments, automating behavioral experiments, Raspberry Pis, design experiments modules, OpenBehavior |
is listed by: OpenBehavior is related to: AutoPilot project |
DOI:10.1101/807693 | Free, Available for download, Freely Available | https://edspace.american.edu/openbehavior/project/autopilot/ | SCR_021518 | Autopilot | 2026-08-09 09:08:00 | 1 | |||||||
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Linear Analysis of Midgut Resource Report Resource Website 1+ mentions |
Linear Analysis of Midgut (RRID:SCR_021255) | LAM | software toolkit, software resource | Software Python package for spatially defined cellular phenotyping using image segmentation data from linearizable tissue.Software quantitative phenotyping tool intended for regionally defined analysis of Drosophila midguts based on objects detected from microscopy images. | Spatially defined cellular phenotyping, image segmentation data, linearizable tissue, Drosophila melanogaster midguts, multiple sample groups | has parent organization: University of Helsinki; Helsinki; Finland | Free, Available for download, Freely available | SCR_021255 | Linear Analysis of Midgut (LAM) | 2026-08-09 09:07:31 | 1 | ||||||||
|
jMRUI Resource Report Resource Website 1+ mentions |
jMRUI (RRID:SCR_021893) | software toolkit, software resource | Software package for advanced time domain analysis of magnetic resonance spectroscopy (MRS) and spectroscopic imaging (MRSI) data. | time domain analysis, magnetic resonance spectroscopy, magnetic resonance spectroscopy data analysis, spectroscopic imaging, spectroscopic imaging data analysis | PMID:11390270 DOI:10.1186/s12859-017-1459-5 |
http://www.jmrui.eu/ | SCR_021893 | 2026-08-09 09:08:18 | 5 | ||||||||||
|
EDTA Resource Report Resource Website 50+ mentions |
EDTA (RRID:SCR_022063) | software toolkit, software resource | Software package to filter out false discoveries in raw TE candidates and generate high quality non redundant TE library for whole genome TE annotations.Produces filtered non redundant TE library for annotation of structurally intact and fragmented elements. | automated whole-genome de-novo, TE annotation, TE library | NSF Plant Genome Research Program ; USDA National Institute of Food and Agriculture ; State of Iowa ; Canada First Research Excellence Fund Ontario |
PMID:31843001 | Free, Available for download, Freely available | SCR_022063 | Extensive de novo TE Annotator | 2026-08-09 09:08:09 | 80 | ||||||||
|
DeepPoseKit Resource Report Resource Website 1+ mentions |
DeepPoseKit (RRID:SCR_021405) | software toolkit, software resource | Software toolkit with high level API for 2D pose estimation of user defined keypoints using deep learning.Written in Python and built using Tensorflow and Keras.Method for pose estimation developed by behavioral scientists at the Max Planck Institute of Animal Behavior. | 2D pose estimation, animal pose estimation, animal behavior, DeepLabCut, Leap, OpenBehavior |
is listed by: OpenBehavior is related to: DeepPoseKit project |
DOI:10.7554/elife.47994 | Free, Available for download, Freely Available | https://edspace.american.edu/openbehavior/project/deepposekit/ | SCR_021405 | 2026-08-09 09:07:57 | 2 | ||||||||
|
Neurokit2 Resource Report Resource Website 100+ mentions |
Neurokit2 (RRID:SCR_021889) | software toolkit, software resource | Software Python package for neurophysiological signal processing. Used to analyze physiological data. | neurophysiological signal processing, analyze physiological data | PMID:33528817 | Free, Available for download, Freely available | https://github.com/neuropsychology/NeuroKit | SCR_021889 | 2026-08-09 09:08:18 | 111 | |||||||||
|
DeepSqueak Resource Report Resource Website 10+ mentions |
DeepSqueak (RRID:SCR_021524) | software toolkit, software resource | Software MATLAB package for high throughput ultrasonic vocalizations detection, classification, and analysis. | data quantification, ultrasonic vocalizations quantification, ultrasonic vocalization, OpenBehavior |
is listed by: OpenBehavior is related to: DeepSqueak project |
DOI:10.1038/s41386-018-0303-6 | Free, Available for download, Freely Available | https://edspace.american.edu/openbehavior/project/deepsqueak/ | SCR_021524 | 2026-08-09 09:08:00 | 15 | ||||||||
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Cell Type Knowledge Explorer Resource Report Resource Website 1+ mentions |
Cell Type Knowledge Explorer (RRID:SCR_022793) | software application, software resource | Software application to examine multimodal data from thousands of cells across 3 mammalian species. | Allen Brain Map, Cell Type Taxonomies, examine multimodal data, cells across mammalian species |
is related to: Common Cell Type Nomenclature is provided by: BICCN is organization facet of: BICCN |
Free, Freely available | SCR_022793 | Allen Brain Map Cell Type Knowledge Explorer | 2026-08-09 09:08:27 | 4 | |||||||||
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mBrainAligner Resource Report Resource Website 1+ mentions |
mBrainAligner (RRID:SCR_022791) | software toolkit, software resource | Software package provides cross modality image registration pipeline to support whole brain mapping projects. Contains three modules: (1) image preprocessing and global registration, (2) Coherent Landmark Mapping (CLM) based automatic registration, and (3) optional semi-automatic refinement. | cross modality image registration, whole brain mapping, image registration |
is provided by: BICCN is organization facet of: BICCN |
Southeast University ; NSFC ; University Synergy Innovation Program of Anhui Province ; NSFC-Guangdong Joint Fund ; Fundamental Research Funds |
PMID:34887551 | Free, Available for download, Freely available | SCR_022791 | 2026-08-09 09:08:24 | 3 | ||||||||
|
Inquisit LAB Resource Report Resource Website 1+ mentions |
Inquisit LAB (RRID:SCR_022151) | software application, software resource | Software tool for designing and administering psychological tests and experiments on computers. | Millisecond Software, designing psychological tests, administering psychological tests, psychological experiments on computers | Restricted | SCR_022151 | Inquisit 6 LAB, Inquisit 5 LAB | 2026-08-09 09:08:10 | 2 | ||||||||||
|
scDblFinder Resource Report Resource Website 100+ mentions |
scDblFinder (RRID:SCR_022700) | software toolkit, software resource | Software package for detection and handling of doublets/multiplets in single cell sequencing data. | single cell sequencing data, doublets detection, multiplets detection, single cell, sequencing data | PMID:35814628 | Free, Available for download, Freely available | https://bioconductor.org/packages/scDblFinder/ | SCR_022700 | 2026-08-09 09:08:22 | 174 | |||||||||
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PreprintMatch Resource Report Resource Website 1+ mentions |
PreprintMatch (RRID:SCR_022302) | software application, software resource | Software tool to match bioRxiv preprints with their corresponding PubMed paper. | match bioRxiv preprints, corresponding PubMed papers | Restricted | SCR_022302 | 2026-08-09 09:07:52 | 1 | |||||||||||
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insane.py Resource Report Resource Website 1+ mentions |
insane.py (RRID:SCR_022317) | software application, software resource | Software tool for generating custom membranes for molecular simulations. Software Python script to setup Martini bilayer systems. | Generating custom membranes, molecular simulations, Martini bilayer system | DOI:10.1021/acs.jctc.5b00209 | Free, Available for download, Freely available | SCR_022317 | 2026-08-09 09:08:13 | 1 | ||||||||||
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reshape2 Resource Report Resource Website 10+ mentions |
reshape2 (RRID:SCR_022679) | software toolkit, software resource | Software R package to flexible rearrange, reshape and aggregate data. Reshape2 is reboot of reshape package. | flexible rearrange data, reshape data, aggregate data |
is listed by: CRAN is related to: reshape is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | SCR_022679 | 2026-08-09 09:08:26 | 21 | ||||||||||
|
Peptides Resource Report Resource Website 10+ mentions |
Peptides (RRID:SCR_022675) | software toolkit, software resource | Software R package to calculate indices and theoretical physicochemical properties of peptides and protein sequences. | physicochemical properties and indices calculations, amino acid sequences, amino acid physiochemical properties calculations |
is listed by: CRAN is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | https://github.com/dosorio/Peptides/ | SCR_022675 | 2026-08-09 09:08:21 | 11 |
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