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http://www.credrivermice.org/

Project to provide Neuroscience Community with mouse strains that are suitable for tissue and cell-type-specific perturbation of gene function in nervous system. NIH Neuroscience Blueprint has established three centers in the USA for generation of genetically modified mice expressing CRE recombinases in nervous system on the C57BJ/6 genetic background. Mouse lines are generated at Cold Spring Harbor Lab, at Scripps Research Institute, and at Baylor College of Medicine.

Proper citation: CRE Driver Network (RRID:SCR_002720) Copy   

•   Source: SciCrunch Registry

http://www.jax.org/smsr/index.html

Resource of special strains of mice that are valuable tools for genetic analysis of complex diseases. They include panels of recombinant inbred (RI) and chromosome substitution (CS) strains.

Proper citation: Special Mouse Strains Resource (RRID:SCR_002885) Copy   

•   Source: SciCrunch Registry

http://www.ouhsc.edu/compmed/documents/DevelopmentofaSpecificPathogenFreeBaboonColony.pdf

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 4th,2023. Program developing a self-sustaining colony of baboons free of all known herpesviruses, four retroviruses, and SV40 for research. When the program is fully developed, they will provide healthy, behaviorally normal, SPF baboons that are free of all known herpes viruses, four retroviruses, and SV40. To accomplish this goal, the center has established in collaboration with co-investigators and consultants serological and PCR tests for each of the 11 target viruses. These baboon viruses include six herpesviruses (analogs of human HSV, VZV, CMV, HHV6, EBV, and HHV8), four retroviruses (simian foamy virus, SRV/D, SIV, and STLV), and SV40. Twenty-four infant baboons are being recruited into the SPF program in each of the first five years, for a final total of at least 66 SPF baboons. All infants will be repeatedly tested for each of the target viruses. At one month of age, larger social groups of 4-6 SPF animals are formed. Beginning at 2-3 years of age, SPF animals will be integrated into larger socially compatible groups. These groups will eventually mature into breeding harems of SPF animals. This approach provides infants with age-matched companions for socialization during their early period of development, minimizes opportunities for transmission of viruses to the infants from adult animals, and allows for the simultaneous elimination of many different viruses from SPF animals.

Proper citation: Development of a Specific-Pathogen-Free Baboon Colony (RRID:SCR_002900) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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://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   

•   Source: SciCrunch Registry

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   

•   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://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   

•   Source: SciCrunch Registry

https://plexon.com/software-downloads/

Software tool used to control Plexon pattern generator for optogenetic stimulation.

Proper citation: Radiant (RRID:SCR_022645) Copy   

•   Source: SciCrunch Registry

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   

•   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/ranger/

Software R package as fast implementation of Random Forests for high dimentional data.

Proper citation: ranger (RRID:SCR_022521) Copy   

•   Source: SciCrunch Registry