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https://cran.r-project.org/web/packages/MIIVsem/index.html

Software R package for estimating structural equation models using instrumental variables.

Proper citation: MIIVsem (RRID:SCR_017444) Copy   

•   Source: SciCrunch Registry

https://www.lenntech.com/calculators/activity/activity-coefficient.htm

Software tool to calculate the activity coefficient of an ion in solution by Lenntech B.V. Determines the ionic strength of solution by using the concentration of ions present in drinking water.

Proper citation: Lenntech activity coefficient calculator (RRID:SCR_016475) Copy   

•   Source: SciCrunch Registry

http://rkscope.sourceforge.net/

Two photon microscope control software with multi area capabilities.

Proper citation: Scope (RRID:SCR_017454) Copy   

•   Source: SciCrunch Registry

https://github.com/vlchaplin/pyRayleighCuda

Python Rayleigh-Sommerfeld integral for acoustics with optional CUDA graphics processing unit (GPU) implementation.

Proper citation: pyRayleighCuda (RRID:SCR_017453) Copy   

•   Source: SciCrunch Registry

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

Software Python package for working with Neurodata stored in Neurodata Without Borders files. Software providing API allowing users to read and create NWB formatted HDF5 files. Developed in support to NWB project with aim of spreading standardized data format for cellular based neurophysiology information.

Proper citation: PyNWB (RRID:SCR_017452) Copy   

•   Source: SciCrunch Registry

http://download.ant-neuro.com/matlab/

Software as an EEGLAB tool used for LIBEEP recordings.

Proper citation: Libeep EEGLAB plugin (RRID:SCR_016334) Copy   

•   Source: SciCrunch Registry

https://woldlab.caltech.edu/wiki/Condor

Condor project maintains, distributes, and supports variety of computing systems that are deployed by commercial and academic interests world wide. Explores social and technical problems of cooperative computing on scales ranging from desktop to world wide computational Grid.

Proper citation: Condor (RRID:SCR_017664) Copy   

•   Source: SciCrunch Registry

https://www.flimfit.org/

Software package for quantitative analysis of large Fluorescence Lifetime Imaging Microscopy (FLIM) data, including global analysis. It is able to routinely analyse multi-well plate FLIM datasets on conventional PC workstations in a reasonable time., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: FLIMfit (RRID:SCR_016298) Copy   

•   Source: SciCrunch Registry

https://github.com/dmis-lab/biobert

Pre-trained biomedical language representation model for biomedical text mining. This repository provides fine-tuning codes of BioBERT, language representation model for biomedical domain, especially designed for biomedical text mining tasks such as biomedical named entity recognition, relation extraction, question answering, etc.

Proper citation: BioBERT (RRID:SCR_017547) Copy   

•   Source: SciCrunch Registry

https://github.com/BioDepot/nbdocker

Software tool as Jupyter Notebook extension for Docker. Each Docker container encapsulates its individual computing environment to allow different programming languages and computing environments to be included in one single notebook, provides user to document code as well as computing environment.

Proper citation: nbdocker (RRID:SCR_017159) Copy   

•   Source: SciCrunch Registry

http://www.agriculturalsoftwareconsultants.com/mixitwin

Professional feed formulation software for Windows 10 and Macs by Agricultural Software Consultants Inc. Complete feed formulation solution for professional nutritionists and feed producers. Software offers ingredient databases for various domesticated and wild species.

Proper citation: MixitWin (RRID:SCR_017553) Copy   

•   Source: SciCrunch Registry

https://github.com/lufuhao/HomoeologPrimer

Software tool as script used to design primers for homoeologs, to amplify either homoeolog specific or all homoeologs.

Proper citation: HomoeologPrimer (RRID:SCR_017559) 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.sqlite.org/index.html

Relational database management system contained in C library. SQLite is not client server database engine but it is embedded into the end program.

Proper citation: SQLite (RRID:SCR_017672) Copy   

•   Source: SciCrunch Registry

https://knowledge.brain-map.org/celltypes

Software application to examine multimodal data from thousands of cells across 3 mammalian species.

Proper citation: Cell Type Knowledge Explorer (RRID:SCR_022793) Copy   

•   Source: SciCrunch Registry

https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/

Software tool to create mutational matrices for all types of somatic mutations. Used to generate mutational matrices for set of samples with associated mutational catalogues. Used for optimized exploration and visualization of mutational patterns for all types of small mutational events. In addition to extending classification of single base substitutions, provides support for classifying doublet base substitutions and small insertions and deletions.

Proper citation: SigProfilerMatrixGenerator (RRID:SCR_023122) Copy   

•   Source: SciCrunch Registry

https://www.millisecond.com/download/

Software tool for designing and administering psychological tests and experiments on computers.

Proper citation: Inquisit LAB (RRID:SCR_022151) Copy   

•   Source: SciCrunch Registry

https://github.com/eegsynth/eegsynth

Open source Python codebase that provides real-time interface between open-hardware devices for electrophysiological recordings like EEG, EMG, and ECG, and analog and digital devices like MIDI, OSC, and analog synthesizers. This allows one to use electrical brain/body activity to flexibly control devices in real-time.

Proper citation: EEGsynth (RRID:SCR_018732) Copy   

•   Source: SciCrunch Registry

https://github.com/PeterEckmann1/preprint-match

Software tool to match bioRxiv preprints with their corresponding PubMed paper.

Proper citation: PreprintMatch (RRID:SCR_022302) Copy   

•   Source: SciCrunch Registry

https://github.com/OpenMendel/MendelIHT.jl

Software Julia package that implements iterative hard thresholding as multiple regression model for GWAS. Built-in support for handling PLINK and VCF files, parallel computing, fits a variety of GLM models, and handles grouping/weighting SNPs.

Proper citation: MendelIHT.jl (RRID:SCR_018292) Copy   

•   Source: SciCrunch Registry