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https://cran.r-project.org/web/packages/ggbreak/vignettes/ggbreak.html
Software package provides several scale functions to break down ‘gg’ plot into pieces and align them together with gap plot or without (wrap plot or cut plot) ignoring subplots. Package was first designed to set breakpoints for truncating plot to shrink outlier long branch of phylogenetic tree. Set Axis Break for ggplot2.
Proper citation: ggbreak (RRID:SCR_024824) Copy
https://github.com/holab-hku/Vulture
Software scalable cloud based pipeline that performs microbial calling for single cell RNA sequencing data, enabling meta analysis of the single cell host microbial studies from AWS Open Data and other public domain.
Proper citation: Vulture (RRID:SCR_024720) Copy
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
Software finite element analysis package. Used to solve field problems.
Proper citation: CalculiX (RRID:SCR_024771) Copy
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
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
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
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
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
https://www.tidyverse.org/blog/2018/11/parsnip-0-0-1/
Software R package to create and manipulate functions commonly used during modeling e.g. fitting the model, making predictions, etc.
Proper citation: Parsnip (RRID:SCR_024744) Copy
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/baycest
Software tool for Bayesian analysis for chemical exchange saturation transfer z-spectra.
Proper citation: BayCEST (RRID:SCR_024951) Copy
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Atlasquery
Software tool designed to allow command line interrogation of atlas images supplied with FSL. It takes as input the name of one of FSL atlases together with either coordinate of interest or mask.
Proper citation: Atlasquery (RRID:SCR_024944) Copy
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
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
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
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
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
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
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
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
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