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https://github.com/abyzovlab/CNVpytor

Software Python package and command line tool for CNV/CNA analysis from depth of coverage by mapped reads. Software tool for CNV/CNA detection and analysis from read depth and allele imbalance in whole genome sequencing.

Proper citation: CNVpytor (RRID:SCR_021627) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/airtrack/

Portal provides head fixed behavioral environment that uses lightweight physical maze floating on air table that moves around animals body under direct control of animal itself.

Proper citation: Airtrack (RRID:SCR_021561) Copy   

•   Source: SciCrunch Registry

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https://github.com/gabraham/flashpca

Software tool as fast principal component analysis of large scale genome wide data. FlashPCA performs fast principal component analysis (PCA) of single nucleotide polymorphism (SNP) data. FlashPCA2 used for principal component analysis of biobank scale genotype datasets.

Proper citation: FlashPCA (RRID:SCR_021680) Copy   

•   Source: SciCrunch Registry

https://github.com/benmurphybaum/StimGen

Software tool as interface for designing and presenting visual stimuli.

Proper citation: StimGen (RRID:SCR_021676) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/signalbuddy/

Portal related to signal generation. Provided system was developed by Columbia University scientists. System includes signal generator for scientific applications which generates digital or true analog signals (sine waves, step functions, and pulse trains) and can be controlled with intuitive serial monitor interface.

Proper citation: SignalBuddy (RRID:SCR_021553) Copy   

•   Source: SciCrunch Registry

https://pycaret.org/

Open source, low code machine learning library in Python that allows you to go from preparing your data to deploying your model within minutes in your choice of notebook environment.

Proper citation: PyCaret (RRID:SCR_021695) Copy   

•   Source: SciCrunch Registry

https://www.nature.com/articles/nprot.2014.131

Software tool calculates direction autocorrelation, plots and calculates other essential parameters to analyze cell migration in two dimensions: it displays cell trajectories individually and collectively, and it calculates average speed and mean square displacements (MSDs) to assess the area explored by cells over time.

Proper citation: DiPer (RRID:SCR_021720) Copy   

•   Source: SciCrunch Registry

https://github.com/kukionfr/VAMPIRE_open

Software tool for analysis of cell and nuclear morphology from fluorescence or bright field images. Enables profiling and classification of cells into shape modes based on equidistant points along cell and nuclear contours. Robust method to quantify cell morphological heterogeneity.

Proper citation: VAMPIRE (RRID:SCR_021721) Copy   

•   Source: SciCrunch Registry

https://github.com/bioinfo-biols/CIRIquant

Software Python package for accurate circRNA quantification and differential expression analysis. Comprehensive analysis pipeline for circRNA detection and quantification in RNA-Seq data. Accurate quantification of circular RNAs identifies extensive circular isoform switching events.

Proper citation: CIRIquant (RRID:SCR_021661) Copy   

•   Source: SciCrunch Registry

https://github.com/kostkalab/scds

Software R package for computational doublet annotation of single cell RNA sequencing data. Software tool for in silico identification of doublets in scRNA-seq data.

Proper citation: Single Cell Doublet Scoring (RRID:SCR_021541) Copy   

•   Source: SciCrunch Registry

http://ufsc.br/

Public university in Florianópolis, the capital city of Santa Catarina in southern Brazil.

Proper citation: Federal University of Santa Catarina; Santa Catarina; Brazil (RRID:SCR_021535) Copy   

•   Source: SciCrunch Registry

https://github.com/flatironinstitute/CaImAn

Open source software tool for scalable calcium imaging data analysis. Used for large scale calcium imaging analysis, including movie handling, motion correction, source extraction, spike deconvolution and result visualization.

Proper citation: Calcium Imaging data Analysis (RRID:SCR_021533) Copy   

•   Source: SciCrunch Registry

https://hackaday.io/project/181604-mri-stereoscope

Project provides miniature mirror stereoscope system for MRI-scanner. System takes advantage of commonly used display equipment, MRI head coil, and display screen. Miniature Wheatstone stereoscope is used for human neuroimaging.

Proper citation: MRI-stereoscope project (RRID:SCR_021655) Copy   

•   Source: SciCrunch Registry

https://spikeforest.flatironinstitute.org/about

Open source and reproducible software suite that benchmarks performance of automated spike sorting algorithms across extensive, curated database of ground truth electrophysiological recordings, displaying results interactively on continuously updating website.

Proper citation: Spike Forest (RRID:SCR_021532) Copy   

•   Source: SciCrunch Registry

https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md

Software tool for accurate, fast and versatile mapping/quantification of single cell and single nucleus RNA-seq data. Used for mapping, demultiplexing and quantification for single cell RNA-seq. Comprehensive turnkey solution for quantifying gene expression in single-cell/nucleus RNA-seq data, built into RNA-seq aligner STAR.

Proper citation: STARsolo (RRID:SCR_021542) Copy   

•   Source: SciCrunch Registry

https://circexplorer2.readthedocs.io/en/latest/

Software package for comprehensive and integrative circular RNA analysis. It is the successor of CIRCexplorer with plenty of new features to facilitate circular RNA identification and characterization. Used to annotate circRNAs, de novo assemble novel circular RNA transcripts and chracterize various of alternative (back-)splicing events of circular RNAs.

Proper citation: CIRCexplorer2 (RRID:SCR_021664) Copy   

•   Source: SciCrunch Registry

https://github.com/mne-tools/mne-cpp

Software tool for real time processing of electrophysiological data.

Proper citation: MNE Scan (RRID:SCR_021530) Copy   

•   Source: SciCrunch Registry

https://services.healthtech.dtu.dk/service.php?NetMHC-4.0

Web tool for binding prediction of peptides to MHC class I molecules. The newest version NetMHC- 4.0 is used for prediction of peptide MHC class I binding affinity using gapped sequence alignment that allows insertions and deletions in alignment.

Proper citation: NetMHC (RRID:SCR_021651) Copy   

•   Source: SciCrunch Registry

https://github.com/yorambenshaul/optimouse

Software tool for analysis of mouse position data.Open source software to analyze positions of individual mice, specifically their nose positions, in behavioral arena with the goal of minimizing error.

Proper citation: Optimouse (RRID:SCR_021527) Copy   

•   Source: SciCrunch Registry

https://github.com/pascalkieslich/mousetrap-os

Integrated, open source mouse tracking software package.Software plugin to record and analyze mouse movements in computerized lab experiments.Software plugin provides two items that implement mouse tracking in OpenSesame.

Proper citation: Mousetrap (RRID:SCR_021523) Copy   

•   Source: SciCrunch Registry