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https://www.thermofisher.com/de/de/home/digital-science/thermo-fisher-connect.html
Platform for connecting people, software, data, and equipment. Helps integrating software, instruments, and data across your lab’s existing ecosystem. Provides: workflows guide users through processes involving multiple systems;Centralized access to Thermo Fisher Scientific instrument service and expertise;Connectivity to monitor and maintain instruments and equipment;Granular data sharing controls to enhance collaboration;Secure environment.
Proper citation: ThermoFisher Connect Platform (RRID:SCR_023441) Copy
Software pipeline for effective HLA data analysis and its application to 145 population samples from Europe and neighbouring areas. Tools for handling and analysing data with ambiquities.
Proper citation: Generate tools (RRID:SCR_023042) Copy
https://github.com/lambdaloop/anipose
Software package for 3D pose estimation. Uses DeepLabCut for 2D tracking and uses triangulation methods to project pose estimations into three dimensions.Toolkit for robust markerless 3D pose estimation.
Proper citation: Anipose (RRID:SCR_023041) Copy
https://github.com/jfarek/xatlas
Software tool as variant caller for SNVs and small indels. Implemented as software application written in C++ .
Proper citation: xAtlas (RRID:SCR_022987) Copy
https://www.starrlifesciences.com/product/small-animal-pulse-oximeter/
Software is part of MouseOx Plus pulse oximeter system.
Proper citation: Starr Life Sciences MouseOx Plus (RRID:SCR_022984) Copy
https://github.com/helioalexandre/MouBeAT
Software package to analyze different behavioral tests in rodents semi-automatically. These tests include Open Field (OF), Elevated Plus Maze (EPM), Y-maze (YM) test and Morris Water Maze (MWM).
Proper citation: Mouse Behavioral Analysis Toolbox (RRID:SCR_023291) Copy
https://pypi.org/project/findmaxima2d/
Software Python 2D Maxima finding algorithm. Re-implementation of Java plugin for ImageJ/Fiji.
Proper citation: findmaxima2d (RRID:SCR_023332) Copy
https://CRAN.R-project.org/package=vcfR
Software R package to read, write, manipulate and analyze variant call format data. Facilitates easy manipulation of variant call format (VCF) data.
Proper citation: vcfR (RRID:SCR_023453) Copy
https://grunwaldlab.github.io/poppr/
Software R package for analysis of populations with mixed modes of sexual and clonal reproduction. Used for genetic analysis of populations with mixed reproduction.
Proper citation: poppr (RRID:SCR_023452) Copy
https://CRAN.R-project.org/package=irrCAC
Software R package to calculate various chance-corrected agreement coefficients among 2 or more raters. Among CAC coefficients covered are Cohen's kappa, Conger's kappa, Fleiss' kappa, Brennan-Prediger coefficient, Gwet's AC1/AC2 coefficients, and Krippendorff's alpha. Multiple sets of weights are proposed for computing weighted analyses.
Proper citation: Computing Chance Corrected Agreement Coefficients (RRID:SCR_023176) Copy
https://CRAN.R-project.org/package=irrICC
Software R package to calculate various intraclass correlation coefficients. Used to quantify inter-rater and intra-rater reliability.
Proper citation: Intraclass Correlations for Quantifying Inter Rater Reliability (RRID:SCR_023175) Copy
https://www.google.com/intl/de/forms/about/
Software for creating surveys and questionnaires.
Proper citation: Google Forms (RRID:SCR_023174) Copy
https://github.com/sapporo-wes/tonkaz
Software CLI tool to verify workflow reproducibility.
Proper citation: Tonkaz (RRID:SCR_023206) Copy
https://github.com/fritzsedlazeck/SURVIVOR
Software tool set for simulating and evaluating SVs, merging and comparing SVs within and among samples, and includes various methods to reformat or summarize SVs. Used for for SV simulation, comparison and filtering.
Proper citation: SURVIVOR (RRID:SCR_022995) Copy
https://github.com/sapporo-wes/yevis-cli
Software CLI tool to support building and maintaining Yevis workflow registry.
Proper citation: Yevis cli (RRID:SCR_023204) Copy
https://CRAN.R-project.org/package=Rtrack
Software R package for analysis of paths from spatial tracking experiments such as Morris water maze and calculation of goal finding strategies. Used for in depth analysis of tracking coordinates from video.
Proper citation: Rtrack (RRID:SCR_023025) Copy
https://www.dtu.ox.ac.uk/homacalculator/
Software tool used to calculate Homeostasis Model Assessment which takes account of variations in hepatic and peripheral glucose resistance, increases in insulin secretion curve for plasma glucose concentrations and contribution of circulating proinsulin. Provides access to HOMA2 model for researchers who wish to use model derived estimates of %B and %S, rather than linear approximations.
Proper citation: HOMA2 calculator (RRID:SCR_023419) Copy
https://www.vitalimages.com/enterprise-imaging-solution/diagnostic-viewer/
Software application providing tools and features that may be used for general purpose radiological viewing and reading of image data from various imaging modalities, clinical review and performs functions of digital image processing, measurement, communications and storage.
Proper citation: Vitrea Read Diagnostic Viewer (RRID:SCR_023418) Copy
https://github.com/marbl/merqury
Software toolkit for reference free quality, completeness, and phasing assessment for genome assemblies. Genome assembly quality evaluation based on k-mers.
Proper citation: Merqury (RRID:SCR_022964) Copy
https://github.com/Kinggerm/GetOrganelle
Software toolkit to assembly of organelle genome from genomic skimming data. Used for accurate de novo assembly of organelle genomes.
Proper citation: GetOrganelle (RRID:SCR_022963) Copy
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