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Software tool for nutrition calculations and surveys.
Proper citation: NutriSurvey (RRID:SCR_022655) Copy
https://github.com/sapporo-wes/sapporo-service
Software for standard implementation conforming to Global Alliance for Genomics and Health Workflow Execution Service API specification.
Proper citation: Sapporo service (RRID:SCR_023202) Copy
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
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://github.com/sapporo-wes/tonkaz
Software CLI tool to verify workflow reproducibility.
Proper citation: Tonkaz (RRID:SCR_023206) 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=ggforce
Software R package providing missing functionality to ggplot2 through extension system introduced with ggplot2 v2.0.0.
Proper citation: ggforce (RRID:SCR_022575) Copy
https://github.com/anuprulez/ml-jupyter-notebook
Open source, docker based, and GPU enabled jupyterlab notebook infrastructure that runs on public compute infrastructure of Galaxy Europe for rapid prototyping and developing end-to-end AI projects. Jupyterlab notebook in GPU enabled docker container for machine learning and deep learning.
Proper citation: Docker based GPU enabled Jupyterlab (RRID:SCR_022695) 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/alexcwsmith/PiRATeMC
Software data management pipeline for camera synchronization and combined data directories.
Proper citation: Pi-based Remote Acquisition Technology for Motion Capture (RRID:SCR_022327) Copy
https://github.com/Frederik-D-Weber/zmax_edf_merge_converter
Software tool for comprehensive conversion of folder with Hypnodyne zmax EDF files into merged European Data Format.
Proper citation: zmax_edf_merge_converter (RRID:SCR_022567) Copy
https://github.com/lufuhao/mitochondria-simulator
Software repository for mtDNA assembly project.
Proper citation: mitochondria simulator (RRID:SCR_023430) Copy
http://szhorvat.net/pelican/igraphm-a-mathematica-interface-for-igraph.html
Software package for use in complex networks and graph theory research. Mathematica interface for igraph. Provides Mathematica interface to popular igraph network analysis package, as well as many other functions for working with graphs in Mathematica. IGraph/M comes pre-packaged and ready to use on Windows, OS X and Linux (64-bit Intel), as well as the Raspberry Pi computer. The code is open source and can be compiled on other platforms as well (such as 32-bit Windows).
Proper citation: iGraph/M (RRID:SCR_023308) Copy
https://github.com/lufuhao/repfinder
Software tool to find shared repeats between mitochondrial genomes.
Proper citation: RepFinder (RRID:SCR_023429) Copy
https://github.com/mgharvey/misc_python/blob/master/bin/TreeMix/treemix_tree_with_bootstraps.py
Phython script for bootstraping Treemix snp trees to generate confidance intervals in the main tree.
Proper citation: treemix_tree_with_bootstraps.py (RRID:SCR_023426) Copy
https://github.com/ggruenhagen3/coselens
Software R package to detect gene level differential selection between two groups of samples.Used for calculation of excess of non synonymous mutations between two groups.
Proper citation: Coselens (RRID:SCR_022578) Copy
https://bioconductor.org/packages/org.Mm.eg.db/
Software package for genome wide annotation for mouse, primarily based on mapping using Entrez Gene identifiers.
Proper citation: org.Mm.eg.db (RRID:SCR_023488) Copy
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