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https://github.com/topepo/caret
Software R package that contains functions for training and plotting classification and regression models. Includes methods for pre-processing training data, calculating variable importance, and model visualizations.
Proper citation: Classification And Regression Training (RRID:SCR_022524) Copy
https://plexon.com/software-downloads/
Software tool used to control Plexon pattern generator for optogenetic stimulation.
Proper citation: Radiant (RRID:SCR_022645) Copy
https://CRAN.R-project.org/package=simplePHENOTYPES
Software R package that simulates pleiotropy, partial pleiotropy, and spurious pleiotropy in wide range of genetic architectures, including additive, dominance and epistatic models. Used to simulate multiple traits controlled by loci with varying degrees of pleiotropy.
Proper citation: simplePHENOTYPES (RRID:SCR_022523) Copy
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://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
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
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://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
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