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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://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://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/sapporo-wes/yevis-cli
Software CLI tool to support building and maintaining Yevis workflow registry.
Proper citation: Yevis cli (RRID:SCR_023204) 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://www.beckman.com/liquid-handlers/software/sami-ex#product-table-wrapper
Software tool provides automation and process control across wide variety of applications, creates planned data driven schedules in optimized and predictable scheduling environment.
Proper citation: SAMI Ex (RRID:SCR_023271) Copy
https://github.com/lufuhao/mitochondria-simulator
Software repository for mtDNA assembly project.
Proper citation: mitochondria simulator (RRID:SCR_023430) Copy
https://www.beckman.com/liquid-handlers/software/dart
Software package that gathers data and synthesizes runtime information from Biomek log files to capture each manipulation of sample during course of method.
Proper citation: Data Acquisition and Reporting Tool (RRID:SCR_023272) 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/compbiolabucf/omicsGAN
Software generative adversarial network to integrate two omics data and their interaction network to generate one synthetic data corresponding to each omics profile that can result in better phenotype prediction. Used to capture information from interaction network as well as two omics datasets and fuse them to generate synthetic data with better predictive signals.
Proper citation: OmicsGAN (RRID:SCR_022976) 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
Software tool for constructing and visualizing bibliometric networks. These networks may for instance include journals, researchers, or individual publications, and they can be constructed based on citation, bibliographic coupling, co-citation, or co-authorship relations. Offers text mining functionality that can be used to construct and visualize co-occurrence networks of important terms extracted from body of scientific literature.
Proper citation: VOSviewer (RRID:SCR_023516) Copy
https://github.com/genome/bam-readcount
Software tool that runs on BAM or CRAM file and generates low level information about sequencing data at specific nucleotide positions. Its outputs include observed bases, readcounts, summarized mapping and base qualities, strandedness information, mismatch counts, and position within the reads.
Proper citation: bam readcount (RRID:SCR_023653) Copy
Software for mouse colony management. Streamlined software for simplified colony management.
Proper citation: Transnetyx Colony Management (RRID:SCR_023922) Copy
https://github.com/wkusmirek/mONiTor
Software tool monitors metrics available in sequencer, state of the computer to which the sequencer is connected, and the contents of the fast5 and fastq files. Real-time monitoring of Oxford Nanopore Technology sequencing run. Used for monitoring nanopore sequencing process.
Proper citation: mONiTor (RRID:SCR_023921) Copy
http://statbio.github.io/Sargasso/
Software Python tool to disambiguate mixed species RNA-seq reads according to their species of origin.
Proper citation: Sargasso (RRID:SCR_023489) Copy
https://github.com/brainglobe/brainreg
Software Python based tool that registers the template brain (e.g. from the Allen Reference Atlas) to the sample image.Automated 3D brain registration with support for multiple species and atlases.
Proper citation: Brainreg (RRID:SCR_023858) Copy
http://bibus-biblio.sourceforge.net/
Bibliographic and reference management software. Allows to search, edit, and sort bibliographic records.
Proper citation: Bibus (RRID:SCR_023974) Copy
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