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https://pypi.org/project/peppy/
Software python package for reading Portable Encapsulated Projects or PEPs in python.
Proper citation: peppy (RRID:SCR_021078) Copy
https://github.com/zhuangjun1981/corticalmapping
Software package for basic visual stimulation, imaging analysis, plotting, and cell visual response properties analysis functionality for calcium imaging.
Proper citation: corticalmapping (RRID:SCR_021871) Copy
https://pypi.org/project/eido/
Software validation tool for Portable Encapsulated Projects or PEPs in python.
Proper citation: eido (RRID:SCR_021076) Copy
https://cran.r-project.org/package=CCP
Software R package for significance tests for canonical correlation analysis, including asymptotic tests and Monte Carlo method.
Proper citation: CCP (RRID:SCR_021745) Copy
https://github.com/portugueslab/stytra
Open source software Python package to control stimulation and track behaviour.Provides timed stimulus presentation, interfacing with external devices and simultaneous real time tracking of behavioral parameters such as position, orientation, tail and eye motion in both freely swimming and head restrained preparations.
Proper citation: Stytra (RRID:SCR_021500) Copy
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
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
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
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
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
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
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
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
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/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
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/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
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
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
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