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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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flyPAD Resource Report Resource Website 1+ mentions |
flyPAD (RRID:SCR_021522) | source code, software resource | FPGA code for running main board of flyPAD. Code written in VHDL using Quartus 2 web edition software. | FPGA code, running main board of flyPAD, VHDL, Quartus 2, OpenBehavior |
is listed by: OpenBehavior is related to: flyPAD project |
DOI:10.1038/ncomms5560 | Free, Available for download, Freely Available | https://edspace.american.edu/openbehavior/project/optopad-and-flypad/ | SCR_021522 | 2026-08-09 09:08:08 | 1 | ||||||||
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sepsis3-amsterdamumcdb Resource Report Resource Website 1+ mentions |
sepsis3-amsterdamumcdb (RRID:SCR_022042) | source code, software resource | Repository contains files for implementing the Sepsis-3 definition in the freely-accessible Amsterdam University Medical Centers Database. | Sepsis-3 criteria, Amsterdam University Medical Centers Database | Restricted | SCR_022042 | Sepsis-3 in AmsterdamUMCdb | 2026-08-09 09:08:09 | 2 | ||||||||||
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pyOS-5 Resource Report Resource Website |
pyOS-5 (RRID:SCR_022336) | source code, software resource | Operant Box code | OpenBehavior, neurophysiology |
is listed by: OpenBehavior is related to: pyOS-5 project |
DOI:10.1038/s41598-021-01717-1 | Free, Available for download, Freely available | https://edspace.american.edu/openbehavior/project/pyos-5/ | SCR_022336 | 2026-08-09 09:08:21 | 0 | ||||||||
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tinglab ureter analysis Resource Report Resource Website |
tinglab ureter analysis (RRID:SCR_022525) | source code, software resource | Analysis code relevant to scRNA sequencing analysis. Code for Fink and Sona et.al. (2022) publication. | Analysis code, scRNA sequencing analysis | Free, Available for download, Freely available | https://doi.org/10.5281/zenodo.6762182 | SCR_022525 | tinglab_ureter_analysis | 2026-08-09 09:07:57 | 0 | |||||||||
|
FlowSorted.Blood.EPIC Resource Report Resource Website 1+ mentions |
FlowSorted.Blood.EPIC (RRID:SCR_022540) | source code, software resource | Software package includes new cell reference for adult peripheral blood deconvolution arrayed using Illumina HumanMethylationEPIC.Optimized library for reference based deconvolution of whole blood biospecimens assayed using Illumina HumanMethylationEPIC BeadArray. | optimized library, reference based deconvolution, whole blood biospecimens | PMID:29843789 | Free, Available for download, Freely available | https://github.com/immunomethylomics/FlowSorted.Blood.EPIC | SCR_022540 | 2026-08-09 09:08:24 | 5 | |||||||||
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CouGaR-g Resource Report Resource Website 1+ mentions |
CouGaR-g (RRID:SCR_022952) | source code, software resource | Source code for "Accurate and Fast Clade Assignment via Deep Learning and Frequency Chaos Game Representation". | Accurate and Fast Clade Assignment, Deep Learning and Frequency Chaos Game Representation, | Free, Available for download, Freely available | SCR_022952 | 2026-08-09 09:08:27 | 1 | |||||||||||
|
Subsemble Cell Type Classifier Resource Report Resource Website |
Subsemble Cell Type Classifier (RRID:SCR_022784) | source code, software resource | Supervised ensemble machine learning classifier. Classification performance benchmark scripts. | Supervised ensemble, machine learning, classifier, cell type classification | Free, Available for download, Freely available | SCR_022784 | 2026-08-09 09:08:04 | 0 | |||||||||||
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Protofilament Bending Models Resource Report Resource Website 1+ mentions |
Protofilament Bending Models (RRID:SCR_023062) | source code, software resource | Code is written to be run with Matlab version r2020b or higher. Model accepts wave assay pulse amplitude data, and simultaneously solves and fits protofilament deflection models to deduce fundamental biophysical properties of microtubule protofilaments. | Matlab, protofilament, microtubule, strain energy, GTP hydrolysis | uses: MATLAB | NIGMS R35GM134842 | DOI:10.7554/eLife.83225 | Free, Available for download, Freely available | SCR_023062 | 2026-08-09 09:08:12 | 1 | ||||||||
|
abSENSE Resource Report Resource Website 1+ mentions |
abSENSE (RRID:SCR_023223) | source code, software resource | Software to interpret undetected homolog.Method that calculates probability that homolog of given gene would fail to be detected by homology search in given species, even if homolog were present and evolving normally. | undetected homolog, gene homolog detection failure, homology search, lineage-specific genes, homology detection failure | Howard Hughes Medical Institute ; NHGRI R01-HG009116; NIGMS RO1-GM43987; NSF 1764269; Simons Center for the Mathematical and Statistical Analysis of Biology 594596; Harvard University |
PMID:33137085 | Free, Available for download, Freely available | http://www.eddylab.org/abSENSE/ | SCR_023223 | 2026-08-09 09:08:33 | 1 | ||||||||
|
PTNet Resource Report Resource Website |
PTNet (RRID:SCR_022975) | source code, software resource | Graph based learning model for protein expression estimation by considering miRNA-mRNA interactions. Estimates protein levels by considering miRNA-mRNA interaction network, mRNA expression and miRNA expression. | protein level, protein expression estimation, miRNA-mRNA interactions, mRNA expression, miRNA expression, | NSF III1755761; NIGMS R01GM113952; NIDDK DK097771 |
DOI:10.1093/bib/bbab264 | Free, Available for download, Freely available | SCR_022975 | 2026-08-09 09:08:28 | 0 | |||||||||
|
BehaviorDEPOT Resource Report Resource Website 1+ mentions |
BehaviorDEPOT (RRID:SCR_023602) | source code, software resource | Software tool for automated behavioral detection based on markerless pose tracking. Behavioral analysis tool to first compile and clean point-tracking output from DeepLabCut, and then classify behavioral epochs using custom behavior classifiers. Used to detect frame by frame behavior from video time series and can analyze results of common experimental assays, including fear conditioning, decision-making in T-maze, open field, elevated plus maze, and novel object exploration. Calculates kinematic and postural statistics from keypoint tracking data from pose estimation software outputs. | OpenBehavior, automated behavioral detection, markerless pose tracking, detect frame by frame behavior, video time series, kinematic and postural statistics, |
is listed by: OpenBehavior is related to: SLEAP, LEAP and MotionMapper project works with: DeepLabCut |
NIMH K01MH116264; NIMH K08MH116125; Whitehall Foundation ; Simonsen Foundation ; NSF ; NIMH T32MH073526; Brain Research Foundation ; Brain and Behavior Research Foundation |
PMID:35997072 | Free, Available for download, Freely available | https://edspace.american.edu/openbehavior/project/behaviordepot/ | SCR_023602 | 2026-08-09 09:08:17 | 2 | |||||||
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22ActionRecognitionTool Resource Report Resource Website 1+ mentions |
22ActionRecognitionTool (RRID:SCR_023552) | source code, software resource | Software tool for multi view child motor development dataset for AI-driven assessment of child development project. | AI-driven assessment, multi view child motor development, child development project, | Free, Available for download, Freely available | SCR_023552 | 2026-08-09 09:08:41 | 1 | |||||||||||
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seqmagick Resource Report Resource Website 1+ mentions |
seqmagick (RRID:SCR_024331) | source code, software resource | Software application to expose file format conversion in BioPython in convenient way. Imagemagick like frontend to Biopython SeqIO. | file format conversion in BioPython, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_11290 | https://sources.debian.org/src/seqmagick/ | SCR_024331 | 2026-08-09 09:08:26 | 2 | ||||||||
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CTDopts Resource Report Resource Website |
CTDopts (RRID:SCR_023997) | source code, software resource | Software gives your command-line tools a CTD-compatible interface. Module for enabling tools with CTD reading/writing, argument parsing, validating and manipulating capabilities. | command-line tools, CTD-compatible interface, module for enabling tools, CTD reading/writing, argument parsing, validating and manipulating capabilities, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/ctdopts/ | SCR_023997 | ctdopts | 2026-08-09 09:08:51 | 0 | ||||||||
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commutator Resource Report Resource Website |
commutator (RRID:SCR_023919) | source code, software resource | Affordable commutator that is equipped with novel sensing system that improves online tracking of cable rotations without impairing the 1-photon calcium imaging via Miniscope. Commutator to allow freely moving behaviors while recording neural activity from platforms such as Miniscope V4 and OpenEphys. Used to perform calcium imaging. | OpenBehavior, sensing system, online tracking, cable rotations, freely moving behaviors, recording neural activity, calcium imaging |
is listed by: OpenBehavior is related to: Freibox |
PMID:37105720 | Free, Available for download, Freely available | https://edspace.american.edu/openbehavior/project/freibox-and-an-open-source-commutator/ | SCR_023919 | open source commutator, commutator, Freibox commutator | 2026-08-09 09:08:43 | 0 | |||||||
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Freibox Resource Report Resource Website |
Freibox (RRID:SCR_023918) | source code, software resource | Versatile open source behavioral system for investigating neuronal correlates of behavioral flexibility via 1-Photon Imaging in freely moving mice. Behavioral testing platform consists of FreiBox, novel low-cost Arduino behavioral setup, controlled by custom Python interface and integrates new licking sensor (strain gauge lickometer) for controlling spatial licking behavioral tasks. | Behavioral testing platform, OpenBehavior, strain gauge lickometer, licking sensor, controlling spatial licking, behavioral task, freely moving mice, |
is listed by: OpenBehavior is related to: commutator has parent organization: University of Freiburg; Baden-Wurttemberg; Germany |
PMID:37105720 | Free, Available for download, Freely available | https://edspace.american.edu/openbehavior/project/freibox-and-an-open-source-commutator/ | SCR_023918 | 2026-08-09 09:08:49 | 0 | ||||||||
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Htscodecs Resource Report Resource Website |
Htscodecs (RRID:SCR_024034) | source code, software resource | Software repository implements the custom CRAM codecs used for "EXTERNAL" block types.Custom compression for CRAM custom algorithm written to compress the BAM file format for DNA sequencing data. | custom CRAM codecs, EXTERNAL" block types, custom compression for CRAM, compress the BAM file format, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/htscodecs/ | SCR_024034 | htscodecs | 2026-08-09 09:08:52 | 0 | ||||||||
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conda-package-handling Resource Report Resource Website |
conda-package-handling (RRID:SCR_023991) | source code, software resource | Software to create and extract conda packages of various formats. | Create and extract conda packages, various formats, conda packages, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/conda-package-handling/, https://conda.github.io/conda-package-handling/ | SCR_023991 | 2026-08-09 09:08:51 | 0 | |||||||||
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ELPH Resource Report Resource Website |
ELPH (RRID:SCR_024011) | source code, software resource | Software tool as general purpose Gibbs sampler for finding motifs in set of DNA or protein sequences.Takes as input a set containing sequences, and searches through them for the most common motif, assuming that each sequence contains one copy of the motif. Used to find patterns such as ribosome binding sites (RBSs) and exon splicing enhancers (ESEs). | Gibbs sampler, finding motifs, DNA sequences, protein sequences, common motif search, find patterns, ribosome binding sites, exon splicing enhancers, | is listed by: Debian | Free, Available for download, Freely available | OMICS_24617 | https://sources.debian.org/src/elph/ | SCR_024011 | Estimated Locations of Pattern Hits, elph | 2026-08-09 09:08:44 | 0 | |||||||
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ms-variability-analysis Resource Report Resource Website 1+ mentions |
ms-variability-analysis (RRID:SCR_024531) | source code, software resource | Variability analysis of proteomics data used for deep learning. | Variability analysis, proteomics data, | Free, Available for download, Freely available | SCR_024531 | 2026-08-09 09:08:29 | 1 |
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