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https://data.caltech.edu/

Data and software repository from CalTech.

Proper citation: CaltechDATA (RRID:SCR_017602) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://vbspt.sourceforge.net/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://mousebytes.ca/home

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://github.com/Ashod/garli

Software application for inferring phylogenetic trees and analysis of molecular sequence data using the maximum-likelihood criterion. It implements nucleotide, amino acid and codon-based models of sequence evolution.

Proper citation: GARLI (RRID:SCR_016117) Copy   

•   Source: SciCrunch Registry

https://web.archive.org/web/20180212152753/http://www.frantz.fi/software/gdpc.php

Software application for visualizing output data from molecular dynamics simulations. It can be customized to read almost any input file format, animate it, and output images of each frame.

Proper citation: gdpc (RRID:SCR_016119) Copy   

•   Source: SciCrunch Registry

https://biosyntax.org/

Software for syntax highlighting for computational biology.

Proper citation: bioSyntax (RRID:SCR_016207) Copy   

•   Source: SciCrunch Registry

http://phonbank.talkbank.org/

Database for study of early phonological development using Phon program. Child phonology component of TalkBank system.

Proper citation: PhonBank (RRID:SCR_016312) Copy   

•   Source: SciCrunch Registry

https://www.nichd.nih.gov/research/supported/NCS/researchers

Data and sample repository for National Children's Study. Provides access to data and samples collected from over 5,600 U.S. birth families to study environmental influences on child health and development. Data and biological and environmental samples are freely available, with approved request, for scientific research.

Proper citation: National Children's Study (NCS) Archive (RRID:SCR_016311) Copy   

•   Source: SciCrunch Registry

https://github.com/kingufl/cOMet

Software for error correction of optical mapping data.

Proper citation: cOMet (RRID:SCR_016276) Copy   

•   Source: SciCrunch Registry

https://www.biomax.com/neuroxm

Software toolkit for semantic integration of multi-modal brain data. It is used to collect, structure, connect, analyze and re-use brain data.

Proper citation: NeuroXM Brain Science Suite (RRID:SCR_016372) Copy   

•   Source: SciCrunch Registry

https://github.com/HicServices/RDMP/wiki

Software toolkit which automates the loading, storage, linkage and provision of data sets. It also cleans, transforms and documents provenance meta-data and domain knowledge to make data sets “research ready”.

Proper citation: Research Data Management Platform (RRID:SCR_016268) Copy   

•   Source: SciCrunch Registry

https://github.com/cortex-lab/Kilosort

Software tool that implements an integrated template matching framework for detecting and clustering spikes from multi-channel electrophysiological recordings.

Proper citation: KiloSort (RRID:SCR_016422) Copy   

•   Source: SciCrunch Registry

http://starbase.sysu.edu.cn/index.php

Web based tool to visualize, analyze, discover and download of large-scale functional genomics data. Used for analysis of the CLIP-Seq and Degradome-Seq data sets, exploration of miRNA–target interactions and decoding RNA interaction networks from CLIP-Seq (HITS-CLIP, PAR-CLIP, iCLIP, CLASH) data. To show RNA-RNA and protein-RNA interaction networks in developmental, physiological and pathological processes.

Proper citation: Starbase V2.0 (RRID:SCR_016303) Copy   

•   Source: SciCrunch Registry

https://fractalis.lcsb.uni.lu/

Software as a scalable open-source service for platform-independent interactive visual analysis of biomedical data. It is a service and a library that work in tandem to equip existing platforms with visual analytical capabilities for explorative data analysis.

Proper citation: Fractalis (RRID:SCR_016362) Copy   

•   Source: SciCrunch Registry

https://github.com/lanagarmire/lilikoi

Software tool as an R package for personalized pathway-based classification modeling using metabolomics data. Provides personalized pathway deregulation measurements (PDS scores) and offers a standardized classification model for biomarker prediction.

Proper citation: lilikoi (RRID:SCR_016361) Copy   

•   Source: SciCrunch Registry