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https://github.com/openworm/tracker-commons

Software tool as repository of documentation, software, and discussions to share worm tracking data and analysis routines.Open access repository for storing, accessing, and filtering data; interchange format for notating single or multi worm behavior; and file formats written in Python for feature extraction, review, and analysis.

Proper citation: Worm Behavior Platform (RRID:SCR_021501) Copy   

•   Source: SciCrunch Registry

https://usegalaxy.eu

Software tools for analysis of data independent acqusition type proteomics data are implemented in Galaxy framework. Enables complete DIA data analysis including spectral library generation based on DDA type data, analysis of DIA data in raw or mzml format, and differntial statistical analysis. All tools are based on open-source software such as diypasef, OpenSwath, swath2stats and MSstats.

Proper citation: Data independent acquisition proteomics workbench (RRID:SCR_021862) Copy   

•   Source: SciCrunch Registry

https://github.com/zeyang-shen/maggie

Software Python package for identifying motifs mediating transcription factor binding and function. Links mutations of motif to changes of epigenomic feature without assuming linear relationship.

Proper citation: Motif Alteration Genome wide to Globally Investigate Elements (RRID:SCR_021903) Copy   

•   Source: SciCrunch Registry

https://github.com/bi-compbio/scrnax/

Software pipeline to improve gene annotation for cross species analysis of single cell RNA-Seq. Cross-species transfer of high quality 3’UTR annotation for single cell RNA-Seq.

Proper citation: scRNAx (RRID:SCR_022091) Copy   

•   Source: SciCrunch Registry

https://github.com/gatech-genemark/ProtHint

Software pipeline for predicting and scoring hints (in form of introns, start and stop codons) in genome of interest by mapping and spliced aligning predicted genes to database of reference protein sequences.

Proper citation: ProtHint (RRID:SCR_021167) Copy   

•   Source: SciCrunch Registry

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

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   

•   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