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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://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
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
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://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
Music composition and manipulation software.
Proper citation: MuseScore (RRID:SCR_016161) 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
http://harvest.readthedocs.org/en/latest/content/harvest-tools.html
Software tools archiving and postprocessing for reference-compressed genomic multi-alignments. It is used for creating and interfacing with Gingr files, which are archives that the Harvest Suite uses to store reference-compressed multi-alignments, phylogenetic trees, filtered variants and annotations.
Proper citation: Harvest-tools (RRID:SCR_016132) Copy
http://CRAN.R-project.org/package=RVAideMemoire
Software package that contains miscellaneous functions useful in biostatistics, such as univariate and multivariate testing procedures with a special emphasis on permutation tests. Many functions shorten existing procedures and implement plotting functions that can be used with a variety of methods and packages.
Proper citation: R package: RVAideMemoire (RRID:SCR_015657) Copy
https://compumedicsneuroscan.com/product/stim2-precise-stimulus-presentation/
Software environment for custom stimulus and task design as well as presentation. Compumedics Neuroscan’s design system which can be integrated in fMRI, MEG, and other functional neuro-imaging applications. Provides interface to design and present visual and auditory stimulation paradigms.
Proper citation: Stim2 (RRID:SCR_016751) Copy
https://www.lenntech.com/calculators/activity/activity-coefficient.htm
Software tool to calculate the activity coefficient of an ion in solution by Lenntech B.V. Determines the ionic strength of solution by using the concentration of ions present in drinking water.
Proper citation: Lenntech activity coefficient calculator (RRID:SCR_016475) Copy
https://www.thermofisher.com/order/catalog/product/CHROMELEON7
Software system to support chromatography operations, to ensure data quality and manage all the analytical processes from instrument control, to raw data storage and processing, through to generating the final results.
Proper citation: Chromeleon Chromatography Data System (CDS) Software (RRID:SCR_016874) Copy
https://github.com/lrq3000/spm_auto_reorient_coregister
Open source cross platform for automatic AC-PC realignment, reorientation and coregistration robust to brain damage in Statistical Parametric Mapping. Set of routines to perform auto reorient and auto coregistration in toolbox SPM12.
Proper citation: spm_auto_reorient_coregister (RRID:SCR_017281) Copy
https://github.com/QTIM-Lab/DeepNeuro
Software Python package for neuroimaging data. Framework to design and train neural network architectures. Used in medical imaging community to ensure consistent performance of networks across variable users, institutions, and scanners.
Proper citation: DeepNeuro (RRID:SCR_016911) Copy
http://rkscope.sourceforge.net/
Two photon microscope control software with multi area capabilities.
Proper citation: Scope (RRID:SCR_017454) Copy
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