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https://genomespy.app/

Software visualization grammar and GPU-accelerated toolkit for genomic data. Visualization grammar and GPU-accelerated rendering engine for genomic data. Grammar based toolkit for authoring tailored, interactive visualizations for genomic data analysis.

Proper citation: GenomeSpy (RRID:SCR_024837) Copy   

•   Source: SciCrunch Registry

https://github.com/bioinform/somaticseq

Software accurate somatic mutation detection pipeline implementing stochastic boosting algorithm to produce somatic mutation calls for both single nucleotide variants and small insertions and deletions. NGS variant calling and classification.

Proper citation: SomaticSeq (RRID:SCR_024891) Copy   

•   Source: SciCrunch Registry

https://www.adobe.com/ca/products/fresco.html

Software digital painting and drawing application. Used to create figures. Built for the latest stylus and touch devices, now including iPhones. Collection of vector and raster brushes, live brushes, to deliver natural painting and drawing experience.Vector and raster graphics editor developed by Adobe primarily for digital painting. Originally designed for the Apple iPad with Pencil support.

Proper citation: Adobe Fresco (RRID:SCR_024887) Copy   

•   Source: SciCrunch Registry

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FAST

Software tool to segment 3D image of brain into different tissue types like Grey Matter, White Matter, CSF, etc., whilst also correcting for spatial intensity variations also known as bias field or RF inhomogeneities. Used to perform tissue type segmentation and bias field correction.

Proper citation: FMRIB's Automated Segmentation Tool (RRID:SCR_024920) Copy   

•   Source: SciCrunch Registry

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FNIRT

Software tool to perform linear registration, meaning that it will translate, rotate, zoom and shear one image to match it with another.

Proper citation: FNIRT (RRID:SCR_024923) Copy   

•   Source: SciCrunch Registry

https://support.qmenta.com/knowledge/sienax-2.6-/-fsl-6.0

Software tool to estimate total brain tissue volume, from single image, normalized for skull size.

Proper citation: SIENAX (RRID:SCR_024926) Copy   

•   Source: SciCrunch Registry

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Cluster

Software application used to form clusters, report information about clusters and/or perform cluster based inference.

Proper citation: fsl-cluster (RRID:SCR_024938) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://daphnia.io/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry