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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/package=mlsbm
Software R package to Fit Bayesian stochastic block models and multi level stochastic block models using efficient Gibbs sampling implemented in Rcpp. Models assume symmetric, non reflexive graphs with unweighted, binary edges. Data are input as symmetric binary adjacency matrix, or list of such matrices.
Proper citation: MLSBM (RRID:SCR_021795) 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/yhoogstrate/bam-lorenz-coverage
Software package to generate Lorenz plots and Coverage plots, directly from BAM file. It can also output tables as text documents so you can generate custom plots. There is also support to only analyse specific regions.
Proper citation: bam-lorenz-coverage (RRID:SCR_021837) Copy
Software package for gradient boosting on decision trees library. Used for ranking, classification, regression and other ML tasks.
Proper citation: Catboost (RRID:SCR_021694) 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
http://membres-timc.imag.fr/Olivier.Francois/LEA/index.htm
Software R package for landscape and ecological associations studies.Dedicated to genomewide association tests in general, with emphasis on association with ecological gradients. Runs analyses of population structure and scans for genomic signatures of local adaptation.
Proper citation: LEA (RRID:SCR_022020) Copy
https://github.com/PacificBiosciences/pb-assembly
Software tool as PacBio assembly tool suite.
Proper citation: pb assembly (RRID:SCR_021967) Copy
Issue
https://cran.r-project.org/package=pcadapt
Software R package for fast Principal Component Analysis for outlier detection.Used to detect genetic markers involved in biological adaptation. Performs genome scans for selection based on principal component analysis.
Proper citation: pcadapt (RRID:SCR_022019) 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
Open source software package for creating and controlling visual environments.Software package for Bonsai which allows for control of 2D and 3D environments.
Proper citation: BonVision (RRID:SCR_021534) Copy
https://github.com/VisionandCognition/Tracker-MRI
Software package for experimental control from Vision and Cognition Lab at Netherlands Institute for Neuroscience. Matlab based software for fMRI, Psychophysical experimentation and NHP training, with eye control using Measurement and Computing IO card. Interfaces with ISCAN eye tracker and communicates with the MRI console using trigger pulses. Uses Psychtoolbox3 graphics and control engine.
Proper citation: Tracker MRI (RRID:SCR_021816) 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://github.com/ModelOriented/randomForestExplainer
Software R package to help explain which variables are most important in random forests. Various variable importance measures are calculated and visualized in different settings in order to get idea on how their importance changes classification or regression model accuracy.
Proper citation: randomForestExplainer (RRID:SCR_021823) Copy
https://bioconductor.org/packages/karyoploteR/
Software R package used to karyoplots. Bioconductor package to plot customizable genomes displaying arbitrary data.
Proper citation: karyoploteR (RRID:SCR_021824) Copy
https://github.com/NollmannLab/qudi-HiM
Software package for control of optical microscope setups with different hardware components optimized to perform multiplexed imaging experiments. Modular laboratory experiment management suite.
Proper citation: qudi-HiM (RRID:SCR_022114) Copy
https://github.com/sqjin/CellChat
Software R toolkit for inference, visualization and analysis of cell-cell communication from single cell data.Quantitatively infers and analyzes intercellular communication networks from single-cell RNA-sequencing data. Predicts major signaling inputs and outputs for cells and how those cells and signals coordinate for functions using network analysis and pattern recognition approaches. Classifies signaling pathways and delineates conserved and context specific pathways across different datasets.
Proper citation: CellChat (RRID:SCR_021946) Copy
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