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https://github.com/ebtrexler/NetSuite
Software for dynamic clamping. It uses National Instruments Boards.
Proper citation: NetClamp (RRID:SCR_016275) Copy
https://github.com/ABCD-STUDY/stroop-task
Software that conducts the Stroop Color Task. Used in the ABCD Study.
Proper citation: stroop-task (RRID:SCR_016033) Copy
https://support.inscopix.com/search/site/Mosaic
Mosaic software features apps designed to help you derive deeper insights from videos of large scale circuit dynamics by Inscopix Inc.
Proper citation: Mosaic (RRID:SCR_017408) Copy
https://michaelbach.de/fract/index.html
Software tool for visual test battery in form of a free computer program.Can be run within your browser or download as a stand-alone program. Used by many vision labs, optometrists and ophthalmologists.
Proper citation: Freiburg Vision Test ('FrACT') (RRID:SCR_016439) Copy
https://cran.r-project.org/web/packages/devtools/index.html
Software tools to make developing R packages easier by providing R functions that simplify and expedite common tasks.
Proper citation: devtools (RRID:SCR_016961) Copy
https://github.com/AllenInstitute/MIES
Software for Electrophysiology functions. It was developed by the Allen Institute.
Proper citation: MIES (RRID:SCR_016443) Copy
https://github.com/lufuhao/ReadCleaner4Scaffolding
This pipeline and the included scripts are used to filter useful reads for SSPACE.
Proper citation: ReadCleaner4Scaffolding (RRID:SCR_016166) Copy
Center that imports, archives, maintains, and distributes mutant mouse alleles as live mice, frozen germplasm, stem cells, and molecular vectors for use in biomedical research. The MMRRC Davis receives transgenics, knockouts, and other kinds of mutant mouse lines at no cost to the donor, and after re-derivation and cryopreservation, distributes breeding stock, germplasm, cells, or tissues of genetically-defined and pathogen-free mice for a small fee to requesting investigators.
Proper citation: University of California at Davis Mutant Mouse Resource and Research Center (RRID:SCR_016448) Copy
http://users.sussex.ac.uk/~lionelb/MVGC/
Matlab software toolkit designed to facilitate Granger-causal analysis with multivariate and possibly multi-trial time series data. Annotated demonstration scripts are available which may be used as templates to assist in this the toolbox's functions.
Proper citation: MVGC Multivariate Granger Causality Matlab Toolbox (RRID:SCR_015755) Copy
http://www.mmrrc.missouri.edu/
Center that supplies mice and conducts research projects focused on the role of mice as animal models. Some of these projects include refinement of models to ensure study reproducibility, as well as development and improvement of economical methods for cryopreservation of mouse strains.
Proper citation: Mutant Mouse Resource and Research Center - University of Missouri (RRID:SCR_016447) Copy
https://github.com/EpistasisLab/ReBATE
Open source software Python package to compare relief based feature selection algorithms used in data mining. Used for feature selection in any bioinformatics problem with potentially predictive features and target outcome variable, to detect feature interactions without examination of all feature combinations, to detect features involved in heterogeneous patterns of association such as genetic heterogeneity .
Proper citation: ReBATE (RRID:SCR_017139) Copy
https://sourceforge.net/projects/icacompass/
Algorithm for MATLAB and the EEGLAB toolbox that enables the automatic detection of independent components from an ICA that represent event-related brain potentials. It performs automatic Independent Component (IC) selection with respect to the contributions of the ICs to a certain ERP.
Proper citation: COMPASS (RRID:SCR_015874) Copy
https://github.com/bionitio-team/bionitio
Open source software tool to provide template for command line bioinformatics tools in various programming languages. Program reads one or more input FASTA files, computes variety of statistics on each file, and prints tabulated output. Used as basis for learning and as foundation for starting new projects.
Proper citation: Bionitio (RRID:SCR_017259) Copy
Software tool as open source programming language to build simple, reliable, and efficient software. Developed by team at Google and many contributors from open source community.
Proper citation: golang (RRID:SCR_017096) Copy
Music composition and manipulation software.
Proper citation: MuseScore (RRID:SCR_016161) Copy
http://sourceforge.net/projects/ipig/
Standalone software tool for the integration of peptide identifications from mass spectrometry experiments into existing genome browser visualizations.
Proper citation: iPiG (RRID:SCR_016164) Copy
https://github.com/ekg/fastahack
Software application for indexing and extracting sequences and subsequences from FASTA files. It will only generate indexes for FASTA files in which the sequences have self-consistent line lengths.
Proper citation: Fastahack (RRID:SCR_016090) Copy
https://github.com/sanger-pathogens/Fastaq
Software application for diverse collection of scripts that perform useful and common FASTA/FASTQ manipulation tasks, such as filtering, merging, splitting, sorting, trimming, search/replace, etc. Input and output files can be gzipped (format is automatically detected) and individual Fastaq commands can be piped together.
Proper citation: Fastaq (RRID:SCR_016091) Copy
Software tool for neuronal recording in intact brain.
Proper citation: Autopatcher (RRID:SCR_017464) Copy
http://fastqtl.sourceforge.net/
Software for mapping of molecular phenotypes that implements a new permutation scheme to accurately and rapidly correct for multiple-testing at both the genotype and phenotype levels in large-scale datasets. It is used to discover quantitative trait loci, multi-dimensional genomic datasets combining DNA-seq and ChiP-/RNA-seq.
Proper citation: Fastqtl (RRID:SCR_016093) Copy
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