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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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CustomCDF Resource Report Resource Website 1+ mentions |
CustomCDF (RRID:SCR_018527) | data processing software, software application, software resource | Brainarray custom CDFs for processing raw Affymetrix data. Used to map probe to probesets. Oligonucleotide probes on GeneChips are reorganized based on latest genome and transcriptome information. | Brainarray, custom CDF, processing raw Affymetrix data, data processing, map probe, probset, oligonucleotide probe, GeneChips, genome, transcriptome, data | PMID:16284200 | Free, Freely available | https://gist.github.com/rmflight/3108891, https://rdrr.io/github/jakejh/metapredict/man/installCustomCdfPackages.html | SCR_018527 | 2026-08-29 11:28:54 | 8 | |||||||||
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ExonerateTransferAnnotation Resource Report Resource Website |
ExonerateTransferAnnotation (RRID:SCR_017557) | data processing software, software application, software resource | Software tool as pipeline to make anntotations using cDNA and CDS sequences. | Exonerate, transfer, annotation, cDNA, CDS, sequence, pipeline, gene | uses: Exonerate | Free, Available for download, Freely available | SCR_017557 | Resource | 2026-08-29 11:28:53 | 0 | |||||||||
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Optimouse project Resource Report Resource Website 1+ mentions |
Optimouse project (RRID:SCR_021463) | data or information resource, portal, project portal | Project related to individual mice positions analysis, specifically their nose positions. Includes software tool for analysis of mouse position data designed by Hebrew University scientists. Provides open source software to analyze positions of individual mice, specifically their nose positions, in behavioral arena with the goal of minimizing error. | Mouse position data analysis, mouse position, position data, nose position, OpenBehavior |
is listed by: OpenBehavior is related to: Optimouse has parent organization: Hebrew University of Jerusalem; Jerusalem; Israel |
DOI:10.1186/s12915-017-0377-3 | Free, Freely available | SCR_021463 | Optimouse | 2026-08-29 11:28:56 | 1 | ||||||||
|
DirectOverlay Resource Report Resource Website 1+ mentions |
DirectOverlay (RRID:SCR_018978) | data processing software, image analysis software, software application, software resource | Software package for display of light microscopy images together with atomic force microscopy images. | Light microscopy, light microscopy image, atomic force microscopy, image, atomic force, microscopy | Restricted | SCR_018978 | 2026-08-29 11:28:55 | 1 | |||||||||||
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Mousetrap project Resource Report Resource Website |
Mousetrap project (RRID:SCR_021456) | data or information resource, portal, project portal | Project related to mouse tracking and analysis of mouse movements during computerized lab experiments. Provides open source software plugin to record and analyze mouse movements. | Record mouse movements, analyze mouse movements, mouse tracking, OpenBehavior |
is listed by: OpenBehavior is related to: Mousetrap |
DOI:10.3758/s13428-017-0900-z | Free, Freely available | SCR_021456 | Mousetrap | 2026-08-29 11:29:02 | 0 | ||||||||
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dadasnake Resource Report Resource Website 1+ mentions |
dadasnake (RRID:SCR_019149) | data processing software, software application, software resource | Software tool as snakemake implementation of DADA2 to process amplicon sequencing data for microbial ecology. | Snakemake, DADA2, amplicon sequencing data, microbial ecology | is related to: DADA2 | DOI:10.1101/2020.05.17.095679 | Free, Available for download, Freely available | SCR_019149 | 2026-08-29 11:29:01 | 4 | |||||||||
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MedParse project Resource Report Resource Website |
MedParse project (RRID:SCR_021455) | data or information resource, portal, project portal | Project related to saving precise times of behavioral events.Provides software tool to read MedPC data into Python and Matlab. | Read MedPC data, Python, Matlab, behavioral events, time event codes, OpenBehavior |
is listed by: OpenBehavior is related to: MedParse |
Free, Freely available | SCR_021455 | MedParse | 2026-08-29 11:28:52 | 0 | |||||||||
|
SpikeForrest Resource Report Resource Website 1+ mentions |
SpikeForrest (RRID:SCR_019261) | data or information resource, portal, project portal | Software reproducible, continuously updating platform which benchmarks performance of spike sorting codes across large curated database of electrophysiological recordings with ground truth. Website and open source computing framework for evaluating and comparing spike sorting algorithms for neurophysiology data analysis. Project of Center for Computational Mathematics at Flatiron Institute. | Spike sorting code performance, electrophysiological recordings, curated database, spike sorting algorithms comparing, spike sorting algorithms evaluation, neurophysiology data analysis, Flatiron Institute | Free, Freely available | SCR_019261 | 2026-08-29 11:28:55 | 2 | |||||||||||
|
CiLiQuant Resource Report Resource Website |
CiLiQuant (RRID:SCR_019319) | data processing software, software application, software resource | Software tool to separate junction reads based on their linear or circular origin. Only non ambiguous junction reads are used to compare relative linear and circular transcript abundance. | RNA, splicing, circular origin, separate junction reads, circular transcript abundance, linear transcript abundance, compare, bio.tools |
is listed by: bio.tools is listed by: Debian |
European Union's Horizon 2020 ; FWO ; Kom Op Tegen Kanker (Stand Up To Cancer) ; Special Research Fund UGent ; Stichting Tegen Kanker |
Free, Available for download, Freely available | biotools:ciliquant | https://bio.tools/ciliquant | SCR_019319 | 2026-08-29 11:29:01 | 0 | |||||||
|
Smart-seq2 Single Sample Pipeline Resource Report Resource Website 1+ mentions |
Smart-seq2 Single Sample Pipeline (RRID:SCR_021228) | data processing software, software application, software resource, software toolkit | Software tool designed by Data Coordination Platform of Human Cell Atlas to process single-cell RNAseq data generated by Smart-seq2 assays.Processes stranded or unstranded, paired- or single-end, scRNA-seq data from an individual cell. | scRNAseq data, Smart-seq2 assays, processing scRNA-seq data from individual cell | has parent organization: Broad Institute | Free, Freely available | https://broadinstitute.github.io/warp/docs/Pipelines/Smart-seq2_Single_Sample_Pipeline/README | https://github.com/broadinstitute/warp/tree/master/pipelines/skylab/smartseq2_single_sample | SCR_021228 | 2026-08-29 11:29:01 | 5 | ||||||||
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Australian Government Data Portal Resource Report Resource Website 1+ mentions |
Australian Government Data Portal (RRID:SCR_019159) | data or information resource, portal | Portal as central source of Australian open government data. Used to find, explore and reuse Australia public data. Anyone can access the anonymised public data published by federal, state and local government agencies, publicly funded research data and datasets from private institutions that are in public interest. | Australian government data, public data, Australia public data, data, unpublised data | Free, Freely available | SCR_019159 | 2026-08-29 11:28:55 | 3 | |||||||||||
|
Gorilla Experiment Builder Resource Report Resource Website 100+ mentions |
Gorilla Experiment Builder (RRID:SCR_020991) | data or information resource, portal | Cloud based research platform that allows researchers and students to quickly and easily create and deploy behavioural experiments online. Online behavioral experiment builder for running behavioural studies. | Reaction time experiments, create behavioural experiments online, behavioural experiment builder, running behavioural studies | Economic and Social Research Council ; Medical Research Council ; Templeton World Charity Foundation |
PMID:31016684 | Free, Freely available | SCR_020991 | 2026-08-29 11:28:51 | 335 | |||||||||
|
Quantifying Animal Movement from Pre-recorded Videos project Resource Report Resource Website |
Quantifying Animal Movement from Pre-recorded Videos project (RRID:SCR_021436) | STL | data or information resource, portal, project portal | Project related to visualizing and quantifying movement from pre-recorded videos. Provides software toolbox for visualizing and quantifying movement.Used for summarizing animal movement data as single image ( spectral time lapse algorithm) as well as automate analysis of animal movement data. | Visualizing movement, quantifying movement, pre-recorded videos movement, summarizing animal movement data, single image, automate analysis, animal movement data, movement tracking, path analysis, video visualization, video summarization, image analysis, OpenBehavior |
is listed by: OpenBehavior is related to: Quantifying Animal Movement from Pre-recorded Videos |
DOI:10.12688/f1000research.3-19.v1 | Free, Freely available | SCR_021436 | Quantifying Animal Movement from Pre-recorded Videos | 2026-08-29 11:28:52 | 0 | |||||||
|
mgatk Resource Report Resource Website 1+ mentions |
mgatk (RRID:SCR_021159) | data processing software, software application, software resource, software toolkit | Software python-based command line interface for processing .bam files with mitochondrial reads and generating high-quality heteroplasmy estimation from sequencing data. This package places a special emphasis on mitochondrial genotypes generated from single-cell genomics data, primarily mtscATAC-seq, but is generally applicable across other assays. | processing .bam files, mitochondrial reads, heteroplasmy estimation, sequencing data, mitochondrial genotypes, mtscATAC-seq | NCI F31 CA232670; NCI P01 CA206978; NCI R01 CA208756; NCI U10 CA180861; NHLBI R33 HL120791; NIDDK R01 DK103794 |
DOI:10.1038/s41587-020-0645-6 | Free, Available for download, Freely available | SCR_021159 | mitochondrial genome analysis toolkit | 2026-08-29 11:29:01 | 4 | ||||||||
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Behavioral Observation Research Interactive Software project Resource Report Resource Website 1+ mentions |
Behavioral Observation Research Interactive Software project (RRID:SCR_021434) | BORIS | data or information resource, portal, project portal | Project related to computer based review of previously recorded videos or live observations. Related to study of animal and human behavior. Provides open source, multiplatform standalone program that allows user specific coding environment for computer based review of previously recorded videos or live observations.Developed by scientists from University of Turin. | Specific coding environment, computer based review, previously recorded videos review, live observations review, OpenBehavior |
is listed by: OpenBehavior is related to: Behavioral Observation Research Interactive Software has parent organization: University of Turin;Turin;Italy |
DOI:10.1111/2041-210x.12584 | Free, Freely available | SCR_021434 | Behavioral Observation Research Interactive Software | 2026-08-29 11:29:02 | 9 | |||||||
|
MRI Compatible and Customizable Microdrive Design for Neuroscience Research Resource Report Resource Website 1+ mentions |
MRI Compatible and Customizable Microdrive Design for Neuroscience Research (RRID:SCR_019247) | data or information resource, portal, project portal | Open source designs for customizable, MRI compatible microdrive capable of positioning probes including stimulating electrodes, recording electrodes, drug cannulae, or optogenetic fibers within brain. Design integrates cranial implant, penetration grid for guiding probes, and microdrive body assembly with actuators. Used by neuroscience community related to electrical microstimulation, neuronal recording, and local drug delivery. | CAD files, microdrive, MRI compatible microdrive, customizable microdrive, 3D printable microdrive, neuroscience research | DOI:10.1523/ENEURO.0495-20.2021 | Free, Freely available | SCR_019247 | 2026-08-29 11:28:55 | 1 | ||||||||||
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Smart-seq2 Single Nucleus Multi Sample Pipeline Resource Report Resource Website 1+ mentions |
Smart-seq2 Single Nucleus Multi Sample Pipeline (RRID:SCR_021312) | data processing software, software application, software resource, software toolkit | Software pipeline for single-nucleus RNAseq data generated by Smart-seq2 assays.Used to simultaneously process multiple libraries of single nuclei Smart-seq2 and Smart-seq4 data. For each library (nucleus), the pipeline trims paired FASTQ files, aligns trimmed reads to the genome, counts intronic and exonic reads, and calculates quality control metrics. Counts and metrics for all libraries are combined into merged Loom formatted count matrix. | snRNAseq data, Smart-seq2 assays, single nucleus, multi sample, WARP repository |
is used by: BICCN has parent organization: Broad Institute has parent organization: Allen Institute has parent organization: University of California at San Diego; California; USA is organization facet of: Terra |
Free, Freely available | https://app.terra.bio/#workspaces/warp-pipelines/Smart-seq2_Single_Nucleus_Muti-Sample | https://github.com/broadinstitute/warp/tree/master/pipelines/skylab/smartseq2_single_nucleus_multisample | SCR_021312 | Multi-snSS2, Smart-seq2 Single Nucleus Multi-Sample Pipeline | 2026-08-29 11:28:51 | 2 | |||||||
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M-Track project Resource Report Resource Website |
M-Track project (RRID:SCR_021433) | data or information resource, portal, project portal | Project related to tracking movement of labelled paws in grooming and freely behaving mice. Provides software toolbox for automated detection of forepaw trajectories in mice. | Automated detection, forepaw trajectories, labelled forepaw, freely behaving mice, freely behaving rats, simultaneous trackcking individual paws, movement, spontaneous grooming episodes, OpenBehavior |
is listed by: OpenBehavior is related to: M-Track |
DOI:10.1371/journal.pcbi.1005115 | Free, Freely available | SCR_021433 | M-Track | 2026-08-29 11:29:02 | 0 | ||||||||
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ModelMatcher Resource Report Resource Website 1+ mentions |
ModelMatcher (RRID:SCR_021208) | data or information resource, portal | Matchmaking platform for clinicians and scientists to facilitate collaborative research on rare and undiagnosed diseases. Used for collaborative projects that advance scientific knowledge and patient care. Currently supports Mouse, Rat, Frog, Zebrafish, Fruit Fly, Nematode Worm, Budding Yeast, Fission Yeast, and E. coli. Used to identify human ortholog of genes in these model organisms and vice versa. Scientists who register in ModelMatcher are asked to classify their genes of interest into Public or Restricted categories.The Match feature will allow Clinicians to obtain information on genes that Scientists classify as both Public and Restricted. | Rare diseases collaborative research, undiagnosed diseases, identify human genes ortholog, genes classification, gene information for clinicians |
is related to: University of British Columbia; British Columbia; Canada has parent organization: Baylor College of Medicine; Houston; Texas |
Free, Freely available | SCR_021208 | 2026-08-29 11:28:55 | 4 | ||||||||||
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Pathfinder project Resource Report Resource Website |
Pathfinder project (RRID:SCR_021447) | data or information resource, portal, project portal | Project to detect spatial navigation behavior in animals.Provides open source software for analyzing spatial navigation search strategies developed by University of British Columbia scientists. | Analyzing spatial navigation search strategies, spatial navigation, search strategies, OpenBehavior |
is listed by: OpenBehavior is related to: Pathfinder has parent organization: University of British Columbia; British Columbia; Canada |
DOI:10.1101/715961 | Free, Freely available | SCR_021447 | Pathfinder | 2026-08-29 11:28:52 | 0 |
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