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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Knowledge based Identification of Pathway Enzymes Resource Report Resource Website 1+ mentions |
Knowledge based Identification of Pathway Enzymes (RRID:SCR_022370) | KIPEs | data processing software, data analysis software, software resource, software application | Software tool as automatic approach for identification of players in biosynthesis pathway. Used for automatic annotation of flavonoid biosynthesis steps in new transcriptome of genome sequence assembly. Various enzymes of entire metabolic networks can be identified if sufficient knowledge about functionally relevant amino acids is available.Combines comprehensive sequence similarity analyses with inspection of functionally relevant amino acid residues and domains in subjected peptide sequences. | Automatic annotation, biosynthesis steps, new transcriptome of genome sequence assembly annotation, biosynthesis pathway, sequence similarity analyses, inspection of functionally relevant amino acid residues, peptide sequences | PMID:32867203 | Free, Available for download, Freely available | SCR_022370 | 2026-08-12 10:52:31 | 2 | |||||||||
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PICRUSt2 Resource Report Resource Website 500+ mentions |
PICRUSt2 (RRID:SCR_022647) | simulation software, software resource, software application | Software for predicting functional abundances based only on marker gene sequences.Used for prediction of metagenome functions. Contains updated and larger database of gene families and reference genomes, provides interoperability with any operational taxonomic unit (OTU)-picking or denoising algorithm, and enables phenotype predictions. Allows addition of custom reference databases. | predicting functional abundances, marker gene sequences, metagenome functions prediction | is related to: PICRUSt | NSF IOS CAREER 1942647; NIDDK U54DK102557; NIDDK R24DK110499; NSERC ; GlaxoSmithKline |
PMID:32483366 | Free, Available for download, Freely available | https://github.com/picrust/picrust2 | SCR_022647 | Phylogenetic Investigation of Communities by Reconstruction of Unobserved States | 2026-08-12 10:52:46 | 583 | ||||||
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Napari Resource Report Resource Website 10+ mentions |
Napari (RRID:SCR_022765) | software resource, data access protocol, web service | Multi dimensional image viewer for Python. Used for browsing, annotating, and analyzing large multi dimensional images. Can be coupled to machine learning and image analysis tools enabling more user friendly automated analysis. | Multi dimensional image viewer, large multi dimensional images, automated analysis | Free, Available for download, Freely available | https://github.com/napari/napari, https://zenodo.org/record/6598542#.YykVuHbMK3A | SCR_022765 | 2026-08-12 10:52:37 | 46 | ||||||||||
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multiHiCcompare Resource Report Resource Website 1+ mentions |
multiHiCcompare (RRID:SCR_022368) | data processing software, data analysis software, software resource, software application | Software package for removing biases across multiple Hi-C datasets. Properly handles Hi-C-specific decay of chromatin interaction frequencies with increasing distance between interacting regions. | detecting priori known chromatin interaction differences, jointly normalized datasets, recover loss of chromatin interactions, Hi-C specific decay of chromatin interaction frequencies, remove bias between multiple Hi-C datasets | American Cancer Society ; NIEHS T32ES007334 |
DOI:10.1093/bioinformatics/btz048 | Free, Available for download, Freely available | https://github.com/dozmorovlab/multiHiCcompare | SCR_022368 | 2026-08-12 10:52:42 | 4 | ||||||||
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MUON Resource Report Resource Website 1+ mentions |
MUON (RRID:SCR_022804) | data processing software, data analysis software, software resource, software application | Software Python framework designed to work with multimodal omics data. Aims to provide convenience and speed to its users enabling standardised analysis while staying flexible and expandable. Muon stands on shoulders of and integrates with annotated data object specification and scanpy library for single cell analysis in Python. | Multimodal omics data, standardised analysis, annotated data object specification, scanpy, single cell analysis, Python | uses: scanpy | Free, Available for download, Freely available | https://github.com/scverse/muon | SCR_022804 | multimodal omics Python framework | 2026-08-12 10:52:56 | 5 | ||||||||
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Megadepth Resource Report Resource Website 1+ mentions |
Megadepth (RRID:SCR_022779) | data processing software, data analysis software, software resource, software application | Software tool for quantifying alignments and coverage for BigWig and BAM/CRAM input files.Quantifies number of RNA-seq reads assigned to gene in BAM file, successor of bamcounts. | quantifying alignments, BigWig and BAM/CRAM input files, RNA-seq reads assigned to gene in BAM file quantification, | NIGMS R01GM118568; NIGMS R01GM121459; UK Medical Research Council |
PMID:33693500 | Free, Available for download, Freely available | https://bioconductor.org/packages/megadepth | SCR_022779 | 2026-08-12 10:52:37 | 2 | ||||||||
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University of Pennsylvania Perelman School of Medicine Penn Medicine BioBank Core Facility Resource Report Resource Website 10+ mentions |
University of Pennsylvania Perelman School of Medicine Penn Medicine BioBank Core Facility (RRID:SCR_022415) | PMBB | material storage repository, service resource, biobank, core facility, storage service resource, access service resource | BioBank supports researchers by providing centralized access to large number of annotated blood and tissue samples. | USEDit, ABRF, annotated blood and tissue samples | is listed by: ABRF CoreMarketplace | ARBF_1421 | https://coremarketplace.org?citation=1&FacilityID=1421 | SCR_022415 | University of Pennsylvania Perelman School of Medicine Penn Medicine BioBank | 2026-08-12 10:52:32 | 16 | |||||||
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Histological E data Registration in rodent Brain Spaces Resource Report Resource Website 1+ mentions |
Histological E data Registration in rodent Brain Spaces (RRID:SCR_022776) | HERBS | data processing software, data visualization software, software resource, software application | Open source, extendable, intuitive and interactive software platform for image visualisation and image registration. Python based GUI for histological E-data registration in brain space. | OpenBehavior, image visualisation, image registration, histological E-data registration, brain space | is listed by: OpenBehavior | DOI:10.1101/2021.10.01.462770 | SCR_022781, https://edspace.american.edu/openbehavior/project/herbs/ | SCR_022776 | 2026-08-12 10:52:47 | 1 | ||||||||
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Adaptive Immune Receptor Repertoire Rearrangement Schema Resource Report Resource Website 1+ mentions |
Adaptive Immune Receptor Repertoire Rearrangement Schema (RRID:SCR_022592) | portal, data or information resource, narrative resource, standard specification, topical portal | Part of AIRR Data Model, defines annotations needed for rearrangements, which are sequences describing rearranged adaptive immune receptor chain (e.g., antibody heavy chain or TCR beta chain). Data for Rearrangement objects are stored as rows in tab delimited file and should be compatible with any TSV reader. Dataset is defined in this context as: TSV file, TSV with companion YAML file containing metadata, or directory containing multiple TSV files and YAML files. | AIRR Data Model, annotations needed for rearrangements, rearranged adaptive immune receptor chain sequences, | is related to: AIRR Data Commons | PMID:29144493 | Free, Freely available | https://fairsharing.org/FAIRsharing.zwjNAh | SCR_022592 | 2026-08-12 10:52:34 | 1 | ||||||||
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OrthoVenn2 Resource Report Resource Website 100+ mentions |
OrthoVenn2 (RRID:SCR_022504) | software resource, data access protocol, web service | Web server for whole genome comparison and annotation of orthologous clusters across multiple species.Works on any operating system with modern browser and Javascript enabled. Used to identify orthologous gene clusters and supports user define species to upload customized protein sequences. Interactive graphic tool which provides Venn diagram view for comparing multiple species protein sequences. | whole genome comparison and annotation, orthologous clusters across multiple species, identify orthologous gene clusters, comparing multiple species protein sequences | National Natural Science Foundation of China | PMID:31053848 | Free, Freely available | SCR_022504 | 2026-08-12 10:52:53 | 288 | |||||||||
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PavCA project Resource Report Resource Website 1+ mentions |
PavCA project (RRID:SCR_022508) | PavCA | data or information resource, topical portal, portal | Project related to tracking behavior. Used to identify subgroups of individuals that differentially attribute incentive value to food cue. Includes apparatus for studying Pavlovian conditioned approach behavior. Customized rat PavCA chambers are constructed based on modular devices purchased from Med-Associates. Code used to operate equipment and collect data was written using Med-Associates’ MEDSTATE programming language. This program is then loaded into Med-PC V operating program, also created by Med-Associates. | Behavior, behavior analysis, Pavlovian conditioning, apparatus, Pavlovian conditioned approach, Instrument, OpenBehavior |
is listed by: OpenBehavior has parent organization: University at Buffalo; New York; USA |
Free, Freely available | SCR_022508 | Pavlovian Conditioned Approach, PavCA | 2026-08-12 10:52:54 | 2 | ||||||||
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Timed pressure control hardware and software for delivery of air mediated distensions in animal models Resource Report Resource Website 1+ mentions |
Timed pressure control hardware and software for delivery of air mediated distensions in animal models (RRID:SCR_022363) | data or information resource, instrument resource, project portal, portal | System uses Arduino microcontroller to control relay module that operates solenoid valve which all sit in 3D printed housing. Solenoid works in conjunction with flowmeter regulator to allow for controlled flow of pressurized air into target. Timing of distensions is controlled via either custom Python based UI, or by triggered TTL pulse.Timed pressure control hardware and software used for delivery of air mediated distensions in animal models. | OpenBehavior, Instrument, behavior apparatus, delivery of air mediated distensions, animal models | is listed by: OpenBehavior | DOI:10.1016/J.OHX.2022.E00271 | Free, Freely available | https://osf.io/rs5p4 | SCR_022363 | Timed pressure control hardware and software for delivery of air mediated distensions in animal models project | 2026-08-12 10:52:30 | 1 | |||||||
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OpenPose Resource Report Resource Website 10+ mentions |
OpenPose (RRID:SCR_022362) | data processing software, data analysis software, software resource, software application | Software tool as multi subject keypoint detection library for real time pose estimation.Used to track behavior of monkeys in natural environments, without disrupting their typical pattern of behavior. Deep learning software system for body, face, hands, and foot estimation in monkeys. | OpenBehavior, tracking limb orientation, behavior measurement, freely moving, realtime recording and analysis, video analysis | is listed by: OpenBehavior | DOI:10.1101/2021.01.28.428726 | Free, Available for download, Freely available | https://github.com/CMU-Perceptual-Computing-Lab/openpose | SCR_022362 | 2026-08-12 10:52:42 | 13 | ||||||||
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TRex Resource Report Resource Website 1+ mentions |
TRex (RRID:SCR_022361) | data processing software, data analysis software, software resource, software application | Open source animal tracking software tool. Used to visually track movement of multiple animals at once. | OpenBehavior, animal tracking, visually track movement | is listed by: OpenBehavior | DOI:10.7554/eLife.64000 | https://github.com/mooch443/trex | SCR_022361 | 2026-08-12 10:52:52 | 2 | |||||||||
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ExonScan Web Server Resource Report Resource Website 1+ mentions |
ExonScan Web Server (RRID:SCR_022516) | software resource, data access protocol, web service | Software framework for modeling sequence motifs based on maximum entropy principle. | modeling sequence motifs, maximum entropy principle | has parent organization: MIT; Cambridge; Massachusetts; United States | PMID:15285897 | Free, Freely available | SCR_022516 | ExonScan | 2026-08-12 10:52:33 | 2 | ||||||||
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ShinyCell Resource Report Resource Website 10+ mentions |
ShinyCell (RRID:SCR_022756) | data processing software, data visualization software, software resource, software application | Software R package to create interactive Shiny based web applications to visualise single cell data via visualising cell information and/or gene expression on reduced dimensions e.g. UMAP, visualising coexpression of two genes on reduced dimensions, visualising distribution of continuous cell information e.g. nUMI / module scores using violin plots / box plots, visualising composition of different clusters / groups of cells using proportion plots and visualising expression of multiple genes using bubbleplots / heatmap.Shiny Interactive Web Apps for Single-Cell Data. | visualise single cell data, visualising cell information, gene expression on reduced dimensions, visualising coexpression of two genes on reduced dimensions, visualising distribution of continuous cell information | works with: Shiny | Free, Available for download, Freely available | SCR_022756 | 2026-08-12 10:52:56 | 24 | ||||||||||
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DLStream Resource Report Resource Website 1+ mentions |
DLStream (RRID:SCR_022359) | data processing software, data analysis software, software resource, software application | Software tool enables closed loop behavioral experiments using deep learning based markerless, real time posture detection.Closed loop behavioral experiment toolkit using pose estimation of body parts. | OpenBehavior, video analysis, behavioral experiment, pose estimation, body parts | is listed by: OpenBehavior | Projekt DEAL | DOI:10.1038/s42003-021-01654-9 | Free, Available for download, Freely available | https://github.com/SchwarzNeuroconLab/DeepLabStream | SCR_022359 | DeepLabStream | 2026-08-12 10:52:42 | 1 | ||||||
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Variational Embedding of Animal Motion Resource Report Resource Website 1+ mentions |
Variational Embedding of Animal Motion (RRID:SCR_022477) | VAME | data processing software, data visualization software, software resource, software application | Software Python tool to cluster behavioral signals obtained from pose estimation tools. Unsupervised probabilistic deep learning framework capable of finding behavioral motifs in pose estimation data. Capable of augmenting quantitative behavioral analyses of data derived from standard pose-estimation software packages. Written based on core functions from DeepLabCut, and readily works with pose data from that package. Can also work with data from other pose estimation packages such as SLEAP. | OpenBehavior, vame, variational embedding of animal motion, pytorch, pose estimation |
is listed by: OpenBehavior is related to: DeepLabCut is related to: SLEAP, LEAP and MotionMapper project |
Free, Available for download, Freely available | https://edspace.american.edu/openbehavior/project/vame/ | SCR_022477 | Variational Animal Motion Embedding, VAME: Variational Embedding of Animal Motion | 2026-08-12 10:52:53 | 3 | |||||||
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ComplexUpset Resource Report Resource Website 10+ mentions |
ComplexUpset (RRID:SCR_022752) | data processing software, data analysis software, software resource, software application | Software R package for visualization of intersecting sets. Used for quantitative analysis of sets, their intersections, and aggregates of intersections. Visualizes set intersections in matrix layout and introduces aggregates based on groupings and queries. | visualization of intersecting sets, set intSections in matrix layout, aggregates based on groupings and queries, quantitative analysis of sets |
uses: ggplot2 is listed by: CRAN |
Austrian Science Fund ; Air Force Research Laboratory and DARPA ; NHGRI K99 HG007583 |
PMID:26356912 | Free, Available for download, Freely available | SCR_022752 | 2026-08-12 10:52:56 | 25 | ||||||||
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ZDOCK Server Resource Report Resource Website 100+ mentions |
ZDOCK Server (RRID:SCR_022518) | software resource, data access protocol, web service | Web tool as protein docking server, based on rigid body docking programs ZDOCK and M-ZDOCK, to predict structures of protein-protein complexes and symmetric multimers. | Protein docking server, ZDOCK, M-ZDOCK, predict structures, protein-protein complexes, symmetric multimers | NIGMS GM084884 | PMID:24532726 | Free, Freely available | SCR_022518 | 2026-08-12 10:52:44 | 137 |
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