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https://github.com/amathislab/DeepDraw

Software application for creating scalable muscle spindles dataset based on kinematic data and define action recognition task as benchmark. Training and analysis of hierarchical neural networks to solve recognition task from muscle spindle inputs.

Proper citation: DeepDraw (RRID:SCR_024840) Copy   

•   Source: SciCrunch Registry

https://github.com/liufan-creat/bulkGAN

Software tool for scRNA and spatial transcriptomics.Used to generate RNA data close to real bulk RNA-seq with constraints of scRNA-seq data, based on keras and tensflow framework.

Proper citation: bulkGAN (RRID:SCR_024798) Copy   

•   Source: SciCrunch Registry

https://github.com/mcelotto/Feature_Info_Transfer

Software application as MATLAB scripts to compute measures of Feature-specific Information Transfer (FIT) and conditional FIT (cFIT). FIT quantifies direction and magnitude of information flow about specific feature S (such as feature of sensory stimulus) between simultaneously recorded brain regions X and Y. cFIT quantifies amount of directed feature information transmitted between regions X and Y that cannot be potentially routed through region Z.

Proper citation: Feature-specific Information Transfer scripts (RRID:SCR_024772) Copy   

•   Source: SciCrunch Registry

https://github.com/mcelotto/LemkeCelottoEtAl_codes_repo

Software code package associated to the paper: Lemke et al. Information flow between motor cortex and striatum reverses during skill learning. 2023. Quantifies information theoretic quantities used in the associated study.

Proper citation: LemkeCelottoEtAl_codes_repo (RRID:SCR_024773) Copy   

•   Source: SciCrunch Registry

https://cellxgene.cziscience.com/

Portal used to find and download any of data sets published on CELLxGENE. Allows to download and visually explore data to understand functionality of human tissues at cellular level. Optimized for finding, exploring, and reusing single cell data. Collections Page lists collections hosted on CELLxGENE Discover and metadata that define tissue, assay, disease, organism, and cell count for each collection. Once you find published dataset of interest on CELLxGENE Discover, you can click on the explore button below the dataset description to explore the cells of that dataset using the CELLxGENE Explorer.

Proper citation: CZ CELLxGENE Discover (RRID:SCR_024894) 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://github.com/STOmics/SGAE

Software graph neural network based tool for spatial domain deciphering. Used for deciphering spatial domains from spatially resolved transcriptomics.

Proper citation: SGAE (RRID:SCR_024803) Copy   

•   Source: SciCrunch Registry

https://github.com/google-deepmind/deepmind-research/tree/master/enformer

Software package provides implementation of the Enformer model and examples on running the model.

Proper citation: Enformer (RRID:SCR_024805) 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://github.com/kundajelab/tfmodisco

Software application as algorithm for identifying motifs from basepair-level importance scores computed on genomic sequence data.

Proper citation: TF-Modisco (RRID:SCR_024811) Copy   

•   Source: SciCrunch Registry

https://data.scilifelab.se

Platform collates tools, databases, information, and other resources that can be useful to researchers and data producing facilities working in the area of data driven life science. Hub for data driven life science research in Sweden.

Proper citation: SciLifeLab Data Platform (RRID:SCR_024865) 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