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https://github.com/cosanlab/facesync

Open source software Python toolbox which automatically synchronizes recorded facial expressions to videos and events such as social interactions.Framework for recording facial expressions with head mounted cameras.

Proper citation: FaceSync (RRID:SCR_021396) Copy   

•   Source: SciCrunch Registry
  

https://github.com/UmSenhorQualquer/d-track/blob/master/docs/source/index.rst

Software package to track object in 3D based on 3D schematics of scene.Semi automatic 3D video tracking technique to analyse movements and routines of aquatic animals with application to captive dolphins.

Proper citation: D-Track (RRID:SCR_021394) Copy   

•   Source: SciCrunch Registry
  

https://www.7-zip.org

Open source software tool as file archiver with high compression ratio.

Proper citation: 7-Zip (RRID:SCR_021270) Copy   

•   Source: SciCrunch Registry
  

https://github.com/DeepLabCut/DeepLabCut

Open source software package for markerless pose estimation. 2D keypoint detection in animals.

Proper citation: DeepLabCut (RRID:SCR_021391) Copy   

•   Source: SciCrunch Registry
  

https://github.com/ModelOriented/randomForestExplainer

Software R package to help explain which variables are most important in random forests. Various variable importance measures are calculated and visualized in different settings in order to get idea on how their importance changes classification or regression model accuracy.

Proper citation: randomForestExplainer (RRID:SCR_021823) Copy   

•   Source: SciCrunch Registry
  

https://bioconductor.org/packages/karyoploteR/

Software R package used to karyoplots. Bioconductor package to plot customizable genomes displaying arbitrary data.

Proper citation: karyoploteR (RRID:SCR_021824) Copy   

•   Source: SciCrunch Registry
  

https://bioconductor.org/packages/release/bioc/html/MetaVolcanoR.html

Software R package to combine differential gene expression results. Differential expression meta analysis tool. Gene expression meta analysis visualization tool. Used to identify genes whose expression is consistently perturbed across several studies., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: MetaVolcanoR (RRID:SCR_018549) Copy   

•   Source: SciCrunch Registry
  

https://docs.pymc.io/

Software Python package for Bayesian statistical modeling and probabilistic machine learning which focuses on advanced Markov chain Monte Carlo and variational fitting algorithms. Allows model specification directly in Python code.

Proper citation: PyMC3 (RRID:SCR_018547) Copy   

•   Source: SciCrunch Registry
  

https://github.com/NollmannLab/qudi-HiM

Software package for control of optical microscope setups with different hardware components optimized to perform multiplexed imaging experiments. Modular laboratory experiment management suite.

Proper citation: qudi-HiM (RRID:SCR_022114) Copy   

•   Source: SciCrunch Registry
  

https://github.com/sqjin/CellChat

Software R toolkit for inference, visualization and analysis of cell-cell communication from single cell data.Quantitatively infers and analyzes intercellular communication networks from single-cell RNA-sequencing data. Predicts major signaling inputs and outputs for cells and how those cells and signals coordinate for functions using network analysis and pattern recognition approaches. Classifies signaling pathways and delineates conserved and context specific pathways across different datasets.

Proper citation: CellChat (RRID:SCR_021946) Copy   

•   Source: SciCrunch Registry
  

https://github.com/PedroMTQ/mantis

Software homology based protein function annotation tool that integrates multiple reference data sources. Custom reference data sources can also be added.Accepts as input aminoacids sequence fasta. Customizable and is available on Linux.

Proper citation: Mantis (RRID:SCR_021001) Copy   

•   Source: SciCrunch Registry
  

https://github.com/cobilab/geco3/

Software tool as DNA compressor that uses neural network to do mixing of experts.

Proper citation: GeCo3 (RRID:SCR_018877) Copy   

•   Source: SciCrunch Registry
  

https://www.openscad.org/

Software tool for creating solid 3D CAD objects. Used for creating 3D models focusing on CAD aspects of 3D modeling of machine parts. Reads in script file that describes object and renders 3D model from this script file.

Proper citation: OpenSCAD (RRID:SCR_018870) Copy   

•   Source: SciCrunch Registry
  

https://www.1ka.si/d/en

Open source software application that enables services for online surveys. Provides advanced support for all steps of web survey process. Conduct research and analysis from beginning to end.

Proper citation: 1KA (RRID:SCR_019283) Copy   

•   Source: SciCrunch Registry
  

https://github.com/leylabmpi/endoR/

Software R package to interpret fitted tree ensemble model.Used to extract and visualize how predictive variables contribute to tree ensemble model accuracy.

Proper citation: endoR (RRID:SCR_021916) Copy   

•   Source: SciCrunch Registry
  

https://github.com/liqiwei2000/BayesEpiModels

Software tool for accessing performance of different epidemiological models, including both growth and compartmental models, in Bayesian framework.

Proper citation: BayesEpiModels (RRID:SCR_019291) Copy   

•   Source: SciCrunch Registry
  

https://github.com/hietakangas-laboratory/LAM

Software Python package for spatially defined cellular phenotyping using image segmentation data from linearizable tissue.Software quantitative phenotyping tool intended for regionally defined analysis of Drosophila midguts based on objects detected from microscopy images.

Proper citation: Linear Analysis of Midgut (RRID:SCR_021255) Copy   

•   Source: SciCrunch Registry
  

https://colororacle.org/

Software tool as free color blindness simulator for Windows, Mac and Linux. Design for Color Impaired. Takes guesswork out of designing for color blindness by showing you in real time what people with common color vision impairments will see.Color Oracle is open source, available on GitHub for Mac and Windows/Java.

Proper citation: Color Oracle (RRID:SCR_018400) Copy   

•   Source: SciCrunch Registry
  

https://www.google.com/sheets/about/

Spreadsheet program included as part of free, web-based software office suite offered by Google within its Google Drive service. Service also includes Google Docs and Google Slides, word processor and presentation program respectively.

Proper citation: Google Sheets (RRID:SCR_017679) Copy   

•   Source: SciCrunch Registry
  

https://www.molinspiration.com/

Broad range of cheminformatics software tools supporting molecule manipulation and processing, including SMILES and SDfile conversion, normalization of molecules, generation of tautomers, molecule fragmentation, calculation of various molecular properties needed in QSAR, molecular modelling and drug design, high quality molecule depiction, molecular database tools supporting substructure and similarity searches. Molinspiration tools are platform independent and may be run on any PC, Mac, UNIX or LINUX machine. Software is distributed in form of engines, which may be used as stand-alone computational engines, used to power web-based tools, or incorporated into larger in-house Java applications.

Proper citation: Molinspiration (RRID:SCR_018525) Copy   

•   Source: SciCrunch Registry