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https://www.quantumbiologyinstitute.org/
Institute that provides resources and researches the concepts and mechanisms which underlie the complexities of biology. In particular, it incorporates concepts in physics and mathematics to resolve, unravel, and explain complex biological mechanisms and conditions.
Proper citation: Quantum Biology Institute (RRID:SCR_015855) Copy
University-affiliated center that promotes research in diabetes and related metabolic and endocrine disorders at Stanford University.
Proper citation: Stanford Diabetes Research Center (RRID:SCR_015856) Copy
http://brainmeta.com/connectivity_cortical_references_web.php
Bibliography for primate cortical connectivity. The page displays the articles by their year of publication and links to PubMed.
Proper citation: Primate Cortical Connectivity Database (RRID:SCR_002468) Copy
https://github.com/a-ludi/dentist
Software as automated pipeline method to close gaps in assemblies with long reads. Used to close assembly gaps using long reads at high accuracy.
Proper citation: DENTIST (RRID:SCR_021856) Copy
https://imbalanced-learn.org/stable/
Software Python package to tackle curse of imbalanced datasets in machine learning.Offers number of re-sampling techniques commonly used in datasets showing strong between class imbalance.
Proper citation: imblearn (RRID:SCR_021698) 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://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://CRAN.R-project.org/package=ggeffects
Software R package to create tidy data frames of marginal effects for ggplot from model outputs. Used to compute marginal effects and adjusted predictions from statistical models and returns result as tidy data frames.
Proper citation: ggeffects (RRID:SCR_022496) Copy
https://CRAN.R-project.org/package=betareg
Software R package for modeling beta distributed dependent variables, e.g., rates and proportions. In addition to maximum likelihood regression (for both mean and precision of beta distributed response), bias corrected and bias reduced estimation as well as finite mixture models and recursive partitioning for beta regressions are provided.
Proper citation: Betareg (RRID:SCR_022494) 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
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/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
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