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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
https://software.broadinstitute.org/cancer/cga/polysolver
Software tool for HLA typing based on whole exome sequencing data and infers alleles for three major MHC class I genes. Enables accurate inference of germline alleles of class I HLA-A, B and C genes and subsequent detection of mutations in these genes using inferred alleles as reference.
Proper citation: Polysolver (RRID:SCR_022278) Copy
https://github.com/holmescao/ANTS_marking_and_analysis_tools
Software tool for marking ant motion trajectories dataset from video. Provided marking software, three data quality analysis scripts, and tracking performance evaluation tool.
Proper citation: ANTS marking and analysis tools (RRID:SCR_022543) Copy
https://github.com/FRED-2/OptiType
Software tool for precision HLA typing from next generation sequencing data.
Proper citation: OptiType (RRID:SCR_022279) Copy
https://github.com/bpucker/KIPEs
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.
Proper citation: Knowledge based Identification of Pathway Enzymes (RRID:SCR_022370) Copy
https://bioconductor.org/packages/release/bioc/html/multiHiCcompare.html
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.
Proper citation: multiHiCcompare (RRID:SCR_022368) Copy
http://sanger-pathogens.github.io/snp-sites/
Software tool to find SNP sites from multi-FASTA alignment file. Can output results in multiple formats for downstream analysis.
Proper citation: SNP-sites (RRID:SCR_022265) Copy
https://edspace.american.edu/openbehavior/project/ezcalcium/
Software package for MATLAB that makes motion correction, segmentation, signal extraction and dimension reduction, analysis, and visualization of calcium imaging data easy to implement. Open source toolbox for analysis of calcium imaging data.
Proper citation: EZcalcium (RRID:SCR_022354) Copy
https://edspace.american.edu/openbehavior/project/guppy/
Software Python toolbox that makes fiber photometry data analysis intuitive and light on programming.Used to measure neural activity of freely behaving animals.
Proper citation: GuPPy (RRID:SCR_022353) Copy
https://github.com/crtwomey/paws
Statistical software platform for automated scoring of pain in mice.Software R package takes paw trajectory data in response to stimulus and provides automated scoring of pain.
Proper citation: Pain Assessment at Withdrawal Speeds (RRID:SCR_022350) Copy
https://edspace.american.edu/openbehavior/project/neuroethology-tools/
Software Python pipeline for automated detection, pose estimation, and behavior classification in socially interacting mice.Used for pose estimation and behavior quantification in pairs of freely behaving mice.
Proper citation: Mouse Action Recognition System (RRID:SCR_022347) Copy
https://edspace.american.edu/openbehavior/project/sipec/
Software pipeline for video analysis. Deep learning Swiss knife for behavioral data analysis.Performs segmentation, identification, pose-estimation and classification of complex behaviour. Used for analysis of behavior of multiple animals in complex environments.
Proper citation: SIPEC (RRID:SCR_022364) Copy
https://edspace.american.edu/openbehavior/project/mmop/
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.
Proper citation: OpenPose (RRID:SCR_022362) Copy
https://edspace.american.edu/openbehavior/project/trex/
Open source animal tracking software tool. Used to visually track movement of multiple animals at once.
Proper citation: TRex (RRID:SCR_022361) Copy
https://edspace.american.edu/openbehavior/project/dlstream/
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.
Proper citation: DLStream (RRID:SCR_022359) Copy
https://edspace.american.edu/openbehavior/project/pyneal/
Open source software package to support rt-fMRI via data in formats generated by Siemens, Philips, and GE. Used to support real time functional magnetic resonance imaging.
Proper citation: Pyneal (RRID:SCR_022333) Copy
https://github.com/djamesbarker/pMAT
Open source software suite for analysis of fiber photometry data.
Proper citation: pMAT (RRID:SCR_022570) Copy
https://www.erim.eur.nl/research-support/meta-essentials/
Software tool for meta analysis. Facilitates integration and synthesis of effect sizes from different studies. Consists of set of workbooks designed for Microsoft Excel that automatically produces all required statistics, tables, figures, and more.
Proper citation: Meta Essentials (RRID:SCR_022464) Copy
https://edspace.american.edu/openbehavior/project/aba/
Software semi automated brain atlas based analysis pipeline for c-Fos immunohistochemical data. Used to analyze c-Fos in multiple brain regions simultaneously.
Proper citation: Atlas Based Analysis (RRID:SCR_022339) Copy
https://edspace.american.edu/openbehavior/project/dbscorer/
Open source, MATLAB based software for forced swim test and tail suspension test video analysis.
Proper citation: DBscorer (RRID:SCR_022334) Copy
https://pypi.org/search/?q=EmaCalc
Software package in Python for statistical analysis of Ecological Momentary Assessment data.
Proper citation: EmaCalc (RRID:SCR_022943) Copy
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