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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://github.com/h2oai/h2o4gpu
Interface to H2O4GPU, collection of GPU solvers for machine learning algorithms.
Proper citation: h2o4gpu (RRID:SCR_022520) Copy
https://CRAN.R-project.org/package=shinythemes
Software R package Themes for use with Shiny.
Proper citation: shinythemes (RRID:SCR_022757) Copy
https://CRAN.R-project.org/package=shinyhelper
Software R package to add markdown helpfiles to shiny apps, using modal dialog boxes, with no need to observe each help button separately.
Proper citation: shinyhelper (RRID:SCR_022755) Copy
https://bids-matlab.readthedocs.io/en/latest/
Software MATLAB/Octave tools to interact with datasets conforming to Brain Imaging Data Structure format.
Proper citation: BIDS-Matlab (RRID:SCR_022292) Copy
https://CRAN.R-project.org/package=ggforce
Software R package providing missing functionality to ggplot2 through extension system introduced with ggplot2 v2.0.0.
Proper citation: ggforce (RRID:SCR_022575) Copy
https://github.com/ZhiGroup/IBD_benchmark
Software package as open source project benchmarks IBD detection tools with multiple measurements.
Proper citation: IBD Detection Tool Benchmark Tool (RRID:SCR_022850) Copy
https://github.com/anuprulez/ml-jupyter-notebook
Open source, docker based, and GPU enabled jupyterlab notebook infrastructure that runs on public compute infrastructure of Galaxy Europe for rapid prototyping and developing end-to-end AI projects. Jupyterlab notebook in GPU enabled docker container for machine learning and deep learning.
Proper citation: Docker based GPU enabled Jupyterlab (RRID:SCR_022695) Copy
http://cns.hkbu.edu.hk/RIDE.htm
Software Matlab based toolbox for temporal decomposition of EEG signal. Used for decomposition, reconstruction, and single trial analysis of event related potentials.
Proper citation: Residue Iteration Decomposition (RRID:SCR_022174) Copy
https://github.com/alexcwsmith/PiRATeMC
Software data management pipeline for camera synchronization and combined data directories.
Proper citation: Pi-based Remote Acquisition Technology for Motion Capture (RRID:SCR_022327) Copy
https://jarvis-mocap.github.io/jarvis-docs/
Software markerless 3D motion capture toolbox. Used for capturing precise 3D motion.
Proper citation: Joint Acquisition, Recording and Voxel based Inference System (RRID:SCR_022723) Copy
https://github.com/Frederik-D-Weber/zmax_edf_merge_converter
Software tool for comprehensive conversion of folder with Hypnodyne zmax EDF files into merged European Data Format.
Proper citation: zmax_edf_merge_converter (RRID:SCR_022567) Copy
https://CRAN.R-project.org/package=ordinal
Software R package implementation of cumulative link models also known as ordered regression models, proportional odds models, proportional hazards models for grouped survival times and ordered logit/probit models.
Proper citation: ordinal (RRID:SCR_022856) Copy
https://github.com/ggruenhagen3/coselens
Software R package to detect gene level differential selection between two groups of samples.Used for calculation of excess of non synonymous mutations between two groups.
Proper citation: Coselens (RRID:SCR_022578) Copy
https://github.com/tlancian/bio_cs
Software package for implementing algorithms proposed in Lanciano et al. "Contrast Subgraphs Allow Comparing Homogeneous and Heterogeneous Networks Derived from Omics Data".
Proper citation: bio_contrast_subgraph (RRID:SCR_022853) Copy
https://github.com/HChai01/ISGPRE
Software package for predicting interferon stimulated human genes.
Proper citation: ISGPRE (RRID:SCR_022730) Copy
https://github.com/jokergoo/EnrichedHeatmap
Software R package for comprehensive visualization of genomic signal associations. Visualizes enrichment of genomic signals on specific target regions. Used to visualize e.g. how histone marks are enriched to specific sites.
Proper citation: EnrichedHeatmap (RRID:SCR_023082) Copy
https://github.com/plaisier-lab/sygnal
Software pipeline to integrate correlative, causal and mechanistic inference approaches into unified framework that systematically infers causal flow of information from mutations to TFs and miRNAs to perturbed gene expression patterns across patients. Used to decipher transcriptional regulatory networks from multi-omic and clinical patient data. Applicable for integrating genomic and transcriptomic measurements from human cohorts.
Proper citation: SYGNAL (RRID:SCR_023080) Copy
https://cran.r-project.org/package=NMF
Software R package for nonnegative matrix factorization. Implements set of already published algorithms and seeding methods, and provides framework to test, develop and plug new/custom algorithms.
Proper citation: Algorithms and Framework for Nonnegative Matrix Factorization (RRID:SCR_023124) Copy
https://yeatmanlab.github.io/pyAFQ/
Software package focused on automated delineation of major fiber tracts in individual human brains, and quantification of tissue properties within the tracts.Software for automated processing and analysis of diffusion MRI data. Automates tractometry.
Proper citation: Automated Fiber Quantification in Python (RRID:SCR_023366) Copy
https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/
Software tool to create mutational matrices for all types of somatic mutations. Used to generate mutational matrices for set of samples with associated mutational catalogues. Used for optimized exploration and visualization of mutational patterns for all types of small mutational events. In addition to extending classification of single base substitutions, provides support for classifying doublet base substitutions and small insertions and deletions.
Proper citation: SigProfilerMatrixGenerator (RRID:SCR_023122) Copy
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