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https://sourceforge.net/projects/r8s/

Software package for estimating absolute rates of molecular evolution and divergence times on phylogenetic tree. Divergence time estimation on phylogenies.

Proper citation: r8s (RRID:SCR_021161) Copy   

•   Source: SciCrunch Registry

https://github.com/KULL-Centre/BME

Software Python package to construct conformational ensemble of biomolecular system by integrating molecular simulations and experimental data. Performs ensemble reweighting using Bayesian Maximum Entropy approach.

Proper citation: BME (RRID:SCR_021953) Copy   

•   Source: SciCrunch Registry

https://artistoo.net

Software toolbox, formerly called CPMjs, as framework to build interactive, explorable simulation models of cells and tissues in web browser. JavaScript library to build interactive Cellular Potts Models as command line applications or in web browser.

Proper citation: Artistoo (RRID:SCR_020983) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/gtsummary/index.html

Software R package creating customizable presentation ready tables, summarizing data sets, regression models, and more. Used for publication ready data summary and analytic result tables.

Proper citation: gtsummary (RRID:SCR_021319) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://catboost.ai/

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   

•   Source: SciCrunch Registry

https://github.com/wtsi-hpag/PretextView

Software tool to enable visualization from PretextMap output. Desktop application for viewing pretext contact maps. OpenGL Powered Pretext Contact Map Viewer.

Proper citation: PretextView (RRID:SCR_022024) Copy   

•   Source: SciCrunch Registry

https://estech.shinyapps.io/prisma_flowdiagram/

Software R package and ShinyApp for producing PRISMA 2020 compliant flow diagrams. ShinyApp for producing PRISMA 2020 compliant flow diagrams.

Proper citation: PRISMA2020 (RRID:SCR_021053) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://github.com/PacificBiosciences/pb-assembly

Software tool as PacBio assembly tool suite.

Proper citation: pb assembly (RRID:SCR_021967) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/plyranges/

Open source software R package for interacting with common Bioconductor classes Ranges and GenomicRanges. Grammar of genomic data transformation. Provides grammatical and consistent way of manipulating these classes to increase accessiblity for new Bioconductor users.

Proper citation: plyranges (RRID:SCR_021324) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/ChIPseeker/

Software package to retrieve nearest genes around peak, annotate genomic region of peak, implements statstical methods for estimate significance of overlap among ChIP peak data sets, and incorporate GEO database for user to compare own dataset with those deposited in database.Several visualization functions are implemented to summarize coverage of peak experiment, average profile and heatmap of peaks binding to TSS regions, genomic annotation, distance to TSS, and overlap of peaks or genes.

Proper citation: ChIPseeker (RRID:SCR_021322) Copy   

•   Source: SciCrunch Registry

https://gbrs.readthedocs.io/en/latest/

Software suite of tools for reconstructing genomes using RNA-Seq data from multiparent population and for quantifying allele specific expression.

Proper citation: GBRS (RRID:SCR_020963) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=survival

Software R package contains core survival analysis routines, including definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, and parametric accelerated failure time models.

Proper citation: survival (RRID:SCR_021137) Copy   

•   Source: SciCrunch Registry

https://pysam.readthedocs.io/en/latest/api.html

Software tool as interface for reading and writing SAM files. Python module to read and manipulate mapped short read sequence data stored in SAM/BAM files. Lightweight wrapper of htslib C-API.

Proper citation: pysam (RRID:SCR_021017) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=caret

Software R package provides misc functions for training and plotting classification and regression models.Contains tools for data splitting, pre-processing, feature selection, model tuning using resampling, and variable importance estimation, as well as other functionality.

Proper citation: caret (RRID:SCR_021138) Copy   

•   Source: SciCrunch Registry

https://github.com/bonvision

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://github.com/ISA-tools/isa-api

Open platform for interoperable life science experimental metadata. Metadata framework as set of community specifications and software tools for enabling discovery, exchange and publication of metadata from experiments in life sciences. Python library for creation, editing, parsing, and validating of ISA-Tab and ISA-JSON formats.Provides programmatic metadata handling functionality to support automation, common interface and interoperable medium between two ISA formats, as well as with other life science data formats required for depositing data in public databases.

Proper citation: ISA API (RRID:SCR_020980) Copy   

•   Source: SciCrunch Registry