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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/XTRACT
Software command line tool for automated tractography. Standardised protocols for automated tractography in human and macaque brain.
Proper citation: XTRACT (RRID:SCR_024933) Copy
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Randomise
Software tool for nonparametric permutation inference on neuroimaging data.
Proper citation: randomise (RRID:SCR_024937) Copy
https://bioconductor.org/packages/combi/
Software R package for simultaneous exploration of multiple datasets. Compositional omics model based visual integration.Used to integrate omics data for visualization, with special focus on compositionality.
Proper citation: combi (RRID:SCR_024986) Copy
https://cran.r-project.org/web/packages/table1/
Software R package to create HTML tables of descriptive statistics, as one would expect to see as the first table in medical epidemiological journal article. Used for generating tables of descriptive statistics in HTML.
Proper citation: table1 (RRID:SCR_024900) Copy
https://github.com/qt-creator/qt-creator?tab=readme-ov-file
Cross-platform, complete Integrated Development Environment for application developers to create applications for multiple desktop, embedded, and mobile device platforms, such as Android and iOS. It is available for Linux, macOS and Windows operating systems. In addition, you can use the experimental WebAssembly plugin to build applications in web format and run them in web browsers.
Proper citation: Qt Creator (RRID:SCR_024883) Copy
https://github.com/arduino/Arduino
Open-source physical computing platform based on I/O board and development environment that implements the Processing/Wiring language. Arduino can be used to develop stand-alone interactive objects or can be connected to software on your computer.
Proper citation: Arduino IDE (RRID:SCR_024884) Copy
https://www.3dhistech.com/research/software-downloads/
Software tool for working with whole slide images. Digital microscope application for supporting histopathological diagnostic workflow and microscope examination process. Advanced slide viewing software used in clinical pathology and research.
Proper citation: 3DHISTECH SlideViewer (RRID:SCR_024885) Copy
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/MELODIC
Software tool to use at both the subject and group level to decompose FMRI data into time courses and spatial maps using Independent Component Analysis. Used to decompose single or multiple 4D data sets into different spatial and temporal components.
Proper citation: Multivariate Exploratory Linear Optimized Decomposition into Independent Components (RRID:SCR_024916) Copy
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FABBER
Software command-line tool for approximate Bayesian inference using generative signal models.
Proper citation: FABBER (RRID:SCR_024917) Copy
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/verbena
Software tool for quantification of perfusion and other haemodynamic parameters from Dynamic Susceptibility Contrast perfusion MRI of the brain.
Proper citation: VERBENA (RRID:SCR_024919) Copy
https://biostat.app.vumc.org/wiki/Main/PowerSampleSize
Software application as interactive program for performing power and sample size calculations. Can determine the sample size needed to detect specified alternative hypothesis with required power, the power with which specific alternative hypothesis can be detected with given sample size, or the specific alternative hypotheses that can be detected with given power and sample size.
Proper citation: PS:Power and Sample Size Calculation (RRID:SCR_024912) Copy
Whole organism atlas utilizing 2D and 3D imaging. Atlas at cellular resolution serves as foundation for characterization of tissue and cellular change in Daphnia.
Proper citation: Daphnia Atlas (RRID:SCR_024913) Copy
https://github.com/xinhe-lab/GSFA
Software R package that performs sparse factor analysis and differential gene expression discovery simultaneously on single cell CRISPR screening data.
Proper citation: Guided Sparse Factor Analysis (RRID:SCR_025023) Copy
https://www.rdocumentation.org/packages/gplots/versions/3.1.3.1
Software R package to create figures.
Proper citation: gplots (RRID:SCR_025035) Copy
https://github.com/dattalab/moseq2-app
Software application as starting point to MoSeq2 package suite. Unsupervised machine learning method which takes inputs from depth cameras in 3D and transforms them into different behavioral motifs which called syllables. Used to extract mouse pose from depth video and model how pose evolves over time.
Proper citation: moseq2-app (RRID:SCR_025031) Copy
https://github.com/EtieM/outLyzer
Software tool for extracting low-allele-frequency tumor mutations from sequencing background noise in clinical practice. Detects variations, specifically low allele frequency variation, in next generation sequencing data.
Proper citation: OutLyzer (RRID:SCR_025120) Copy
https://sites.google.com/site/plaresmedima/
Software tool to support translation of basic research in medical image analysis into early clinical studies.
Proper citation: PMI (RRID:SCR_025084) Copy
https://github.com/BlankenbergLab/gmxtras/tree/main
Software tool as set of Python scripts to modify GROMACS topology files, by adding content from different topology files and other GROMACS input files. Useful, particularly when system components are assembled outside of GROMACS, or in different steps within GROMACS. This helps prevent users from having to copy and paste significantly large blocks of text within topology files.
Proper citation: GROMACS topology editors (RRID:SCR_025013) Copy
https://CRAN.R-project.org/package=nricens
Software R package for calculating Net Reclassification Improvement for risk prediction models with time to event and binary data. NRI for risk prediction models with time to event and binary response data.
Proper citation: nricens (RRID:SCR_025138) Copy
https://github.com/luo-xiaolong/GSC
Software tool for lossless compression of VCF files, designed to efficiently store and manage VCF files in compressed format. It accepts VCF/BCF files as input and utilizes advanced compression techniques to significantly reduce storage requirements while ensuring fast query capabilities.
Proper citation: Genotype Sparse Compression (RRID:SCR_025071) Copy
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