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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://cran.r-project.org/web/packages/ranger/
Software R package as fast implementation of Random Forests for high dimentional data.
Proper citation: ranger (RRID:SCR_022521) Copy
https://bbknn.readthedocs.io/en/latest/
Software to identify each cell’s top neighbours in each batch separately instead of entire cell pool with no accounting for batch. Nearest neighbours for each batch are then merged to create final list of neighbours for cell. Aligns batches in a quick and lightweight manner.
Proper citation: BBKNN (RRID:SCR_022807) Copy
https://github.com/satijalab/sctransform
Software R package for normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression.
Proper citation: sctransform (RRID:SCR_022146) Copy
https://gitlab.com/maaly7/emerald_metagenomics_annotations
Software metagenomics annotations pipeline that regularly enrich up-to-date ENA and MGnify metagenomics studies with metadata extracted from research articles in EuropePMC.
Proper citation: EMERALD METAGENOMICS ANNOTATIONS PIPELINE (RRID:SCR_022541) Copy
https://github.com/jkimlab/PLR-GEN
Software package for generation of pseudo long reads by using short reads of metagenomic sample and microbial reference genome sequences as input.
Proper citation: PLR-GEN (RRID:SCR_022264) Copy
https://stringr.tidyverse.org/
Software package to provide set of functions designed to make working with strings easy. Consistent wrappers for common string operations.
Proper citation: stringr (RRID:SCR_022813) Copy
Open source parametric 3D modeler to design real life objects of any size. Parametric modeling allows modify your design by going back into your model history and changing its parameters.
Proper citation: FreeCAD (RRID:SCR_022535) Copy
https://github.com/kalininalab/d-StructMAn
Software tool provides annotation of non-synonymous single nucleotide variants in context of structural properties of resulting amino acid changes in corresponding proteins. Improved implementation of StructMAn, shipped in container form and extended to annotation of short in-frame indels and alterations arising as consequence of alternative splicing events. Produces range of structural features by combining information from experimentally resolved structures of many related proteins, which is unique feature of StructMAn family tools. Can also harness all protein structure models stored in AlphaFold Protein Structure Database.
Proper citation: d-StructMAn (RRID:SCR_022534) Copy
Software cross platform mobile application that supports 2D/3D/4D image visualization, multi-morphometry annotation, proofreading, interactive imaging system controlling, and distributed collaboration.
Proper citation: Hi5App (RRID:SCR_022819) Copy
https://github.com/replikation/What_the_Phage
Parallel multitool approach for phage prediction combined with annotation and classification downstream strategy. Used for identification and analysis of phage sequences. Phage identification via nextflow and docker or singularity.
Proper citation: What the Phage (RRID:SCR_022871) Copy
https://github.com/SydneyBioX/SurvBenchmark_package
Software package for comprehensive benchmarking study of survival analysis methods using both omics data and clinical data. Evaluates diverse collection of survival models for both clinical and omics datasets.
Proper citation: SurvBenchmark (RRID:SCR_022503) Copy
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
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