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https://github.com/srp33/ShinyLearner
Software framework for performing benchmarks of machine learning classification algorithms. Containerized benchmarking tool for machine-learning classification of tabular data.
Proper citation: ShinyLearner (RRID:SCR_017608) Copy
https://github.com/SilverLabUCL/SilverLab-Microscope-Software
Software for use with compact Acousto-Optic Lens Microscope (AOLM) developed in the Silver Lab at UCL. Written in LabVIEW. Performs multiple imaging modes and protocols including Z-stacks, multi-plane, single-plane, sub-volume, patches and points. It comes with tools for visualising data acquired with system.
Proper citation: Silver Lab Microscopy Software (RRID:SCR_017456) Copy
Software package for analysis of single particle diffusion trajectories, where diffusion constants switch randomly according to Markov process. Analytical tool to combine information from thousands of short single-molecule trajectories of intracellularly diffusing proteins. Has ability to learn number of diffusive states directly from data, in addition to model parameters such as transition rates and diffusion constants.
Proper citation: vbSPT (RRID:SCR_017554) Copy
https://www.adinstruments.com/products/labchart
LabChart data analysis software creates a platform for all of your recording devices to work together, allowing you to acquire biological signals from multiple sources simultaneously and apply advanced calculations and plots as your experiment unfolds. LabChart Reader is free version of software that allows to analyse with some limitations. LabChart Reader doesn’t allow saving of data - export image only. Has data pad for analysis.
Proper citation: LabChart Reader (RRID:SCR_017551) Copy
Open access database for all cognitive data collected from touchscreen related tasks. Performs data comparison and interactive data visualization for any data uploaded onto the site. There are also guidelines and video tutorials available.
Proper citation: Mousebytes (RRID:SCR_017904) Copy
https://github.com/nci/drishti
Open source scientific visualisation software. Multi platform, volume exploration and presentation software. Used for visualising volumetric data, such as tomography data, electron microscopy data, etc.
Proper citation: Drishti (RRID:SCR_017999) Copy
https://www.volumegraphics.com/de/produkte/vgstudio.html
Software tool for analysis and processing of µCT data, e.g. compiling virtual 3D models of morphological structures in site by Volume Graphics GmbH. Used for visualization of CT data.
Proper citation: VG Studio MAX (RRID:SCR_017997) Copy
https://CRAN.R-project.org/package=webchem
Open source software package for R programming language that is used to acquire chemical information from online data sources. Package contains functions that allow programmer to interact with webpages and APIs to retrieve chemical information.
Proper citation: webchem (RRID:SCR_017684) Copy
Open source software application with data analysis tools and spreadsheet templates used to manage, process and visualize data. LibreOffice Calc is spreadsheet component of LibreOffice software package developed by Document Foundation.
Proper citation: LibreOfficeCalc (RRID:SCR_018013) Copy
https://github.com/shanemomara/omaraneurolab/tree/master/NeuroChaT
Software open source python toolbox to analyse neuronal signals recorded in vivo in freely behaving animal, with particular emphasis on spatial coding. Can be used as application programming interface, or as general user interface, and is designed to help simplify adoption of standardised analyses for behavioural neurophysiology and facilitate open data sharing and collaboration between laboratories.
Proper citation: NeuroChaT (RRID:SCR_018020) Copy
http://sourceforge.net/projects/cnv-webstore
Integrated platform to analyse, store, visualise and interpret CopyNumber Variation data. Analysis is supported for Illumina data, all CNV-reports and raw data can be imported after third-party analysis. Platform to streamline processing and downstream interpretation of microarray data in clinical context. Analysis tools include CNV analysis, parent of origin and uniparental disomy detection. Interpretation tools include data visualisation, gene prioritisation, automated PubMed searching, linking data to several genome browsers and annotation of CNVs based on several public databases.
Proper citation: CNV webstore (RRID:SCR_018007) Copy
https://www.mbfbioscience.com/microdynamix
Software tool for dendritic spine analysis that enables to visualize and quantify spine morphology over time. After loading image data acquired at different time points from in vivo and in vitro imaging sessions, automatically aligns images in 3D, then reconstructs dendritic branches, detects dendritic spines, and identifies important metrics such as length, thickness, and overall number, for accurate quantitative comparison.
Proper citation: MicroDynamix (RRID:SCR_017671) Copy
https://www.mbfbioscience.com/vesalius
Software tool as ultra fast, multi channel resonant scanning laser confocal microscope system for rapid 2D and 3D slide scanning, and cleared tissue imaging. System for imaging of slide mounted specimens and cleared tissue imaging. Utilizes strip mosaic scanning process to rapidly and accurately collect fluorescent image data while stage moves specimen continuously in y-axis.
Proper citation: Vesalius (RRID:SCR_017670) Copy
Open source project to harness scientific and public health potential of pathogen genome data. Provides continually updated view of publicly available data alongside powerful analytic and visualization tools for use by community. Used to aid epidemiological understanding and improve outbreak response. Open source SARS-CoV-2 genome data and analytic and visualization tools.
Proper citation: Nextstrain (RRID:SCR_018223) Copy
https://github.com/AllenInstitute/AllenSDK
Software tool as code for processing and analyzing data in Allen Brain Atlas. Source code for reading and processing Allen Brain Atlas data. Allen SDK focuses on Allen Brain Observatory, Cell Types Database, and Mouse Brain Connectivity Atlas.
Proper citation: Allen Software Development Kit (RRID:SCR_018183) Copy
http://www.cbs.dtu.dk/services/NetMHCpan/
Web server for quantitative prediction of peptide binding to any MHC molecule of known sequence using artificial neural networks. Characterizes binding specificity of given major histocompatibility complex molecule and predicts peptide length profile and peptide binding affinity. NetMHCpan 3.0 is improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length data sets. NetMHCpan 4.0 is trained on naturally eluted ligands and on peptide binding affinity data. NetMHCpan-4.1 server predicts binding of peptides to any MHC molecule of known sequence using artificial neural networks (ANNs).
Proper citation: NetMHCpan Server (RRID:SCR_018182) Copy
http://www.imgt.org/IMGTrepertoire/
Web resource for immunoglobulins (IG), T cell receptors (TR) and major histocompatibility (MH) and related proteins of immune system (RPI). Comprises LIGM expertized data on immunoglobulins (IG), T cell receptors (TR) and major histocompatibility (MH) and related proteins of immune system.
Proper citation: IMGT Repertoire (RRID:SCR_018220) Copy
Software package for analysis of expression dynamics in single cell RNA seq data. Enables estimations of RNA velocities of single cells by distinguishing unspliced and spliced mRNAs in standard single-cell RNA sequencing protocols. Estimates RNA velocity in single cell RNA sequencing datasets. RNA velocity estimation in Python or R.
Proper citation: Velocyto (RRID:SCR_018167) Copy
https://github.com/astroML/astroML
Software Python package for machine learning, statistics and data mining. Contains library of statistical and machine learning routines for analyzing astronomical data in Python, loaders for several open astronomical data sets, and examples of analyzing and visualizing astronomical data sets. Repository of common tools and routines used for statistical data analysis in astronomy and astrophysics.
Proper citation: astroML (RRID:SCR_018138) Copy
https://github.com/r3fang/SnapTools
Software tool as module for working with snap files in Python. Snap files are designed for storing single nucleus ATAC-seq datasets.
Proper citation: SnapTools (RRID:SCR_018097) Copy
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