Tools   Select Another Resource Report Type

https://bioconductor.org/packages/org.Mm.eg.db/

Software package for genome wide annotation for mouse, primarily based on mapping using Entrez Gene identifiers.

Proper citation: org.Mm.eg.db (RRID:SCR_023488) Copy   

•   Source: SciCrunch Registry

https://github.com/Shenhav-and-Korem-labs/SCRuB

Software R package to help researchers address common issue of contamination in microbial studies. Well aware MiSeq decontamination program.

Proper citation: SCRuB (RRID:SCR_023518) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=BoutrosLab.plotting.general

Software R package contains several plotting functions such as barplots, scatterplots, heatmaps, as well as functions to combine plots and assist in creation of these plots. Functions to create publication quality plots.

Proper citation: BPG (RRID:SCR_023652) Copy   

•   Source: SciCrunch Registry

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

Software package implements Bayesian multilevel models in R using probabilistic programming language Stan.

Proper citation: brms (RRID:SCR_023862) Copy   

•   Source: SciCrunch Registry

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

Software R package for calculating and drawing variable trees. Variable trees display information about nested subsets of data frame.

Proper citation: vtree (RRID:SCR_023458) Copy   

•   Source: SciCrunch Registry

https://github.com/PolarBean/DeepSlice?

Software Python package which aligns histology to the Allen Brain Atlas and Waxholm rat atlas using deep learning.

Proper citation: DeepSlice (RRID:SCR_023854) Copy   

•   Source: SciCrunch Registry

http://mouse.brainarchitecture.org/cell-type-analysis-toolbox

Software toolbox is cell counting and distribution mapping platform which can be used to analyze serial two-photon tomography (STPT) data.

Proper citation: Cell Type Analysis Toolbox (RRID:SCR_023852) Copy   

•   Source: SciCrunch Registry

https://github.com/Cristianetaniguti/Reads2Map

Software package as collection of WDL workflows to build linkage maps from sequencing reads. WDL workflows to build genetic maps from sequencing reads.

Proper citation: Reads2Map (RRID:SCR_023593) Copy   

•   Source: SciCrunch Registry

https://github.com/industrial-optimization-group/DESDEO

Software Python framework for interactive multiobjective optimization methods.

Proper citation: DESDEO (RRID:SCR_023502) Copy   

•   Source: SciCrunch Registry

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

Software R package used for searching for optimal clustering procedure for data set.

Proper citation: clusterSim (RRID:SCR_023743) Copy   

•   Source: SciCrunch Registry

https://frictionlessdata.io/

Open source software package for building data infrastructure including data management, data integration, data flows, etc. Includes various data standards and provides software to work with data.

Proper citation: Frictionless Data (RRID:SCR_023713) Copy   

•   Source: SciCrunch Registry

https://github.com/statgen/Rprs

Software R package for computing Polygenic Risk Scores from dosages.

Proper citation: Rprs (RRID:SCR_023557) Copy   

•   Source: SciCrunch Registry

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

Software R package for query NCBI Entrez and retrieve PubMed records in XML or text format. Used to process PubMed records by extracting and aggregating data from selected fields. Large number of records can be downloaded via this simple-to-use interface to NCBI PubMed API. Used to search and retrieve scientific publication records from PubMed.

Proper citation: easyPubMed (RRID:SCR_023570) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/oligo.html

Software R package to analyze oligonucleotide arrays at probe level. Supports Affymetrix (CEL files) and NimbleGen arrays (XYS files). Used for annotation of Affymetrix Gene Array data.

Proper citation: Preprocessing tools for oligonucleotide arrays (RRID:SCR_023726) Copy   

•   Source: SciCrunch Registry

https://github.com/SainsburyWellcomeCentre/ara_tools

Software package for analysis of mouse brain STP data with respect to the Allen Reference Atlas. Collection of MATLAB functions to analyze mouse whole brain imaging data and the associated "sparse" point data such as cell locations, traced neurite trees, or traced projections from a bulk injection. This package relates sparse data to the Allen Mouse Brain Reference Atlas.

Proper citation: ARA Tools (RRID:SCR_023826) Copy   

•   Source: SciCrunch Registry

http://virusdetect.feilab.net/cgi-bin/virusdetect/index.cgi

Software package to efficiently and exhaustively analyze large scale sRNA datasets for virus identification. Automated pipeline for virus discovery using deep sequencing of small RNAs.

Proper citation: VirusDetect (RRID:SCR_023669) Copy   

•   Source: SciCrunch Registry

https://github.com/GuillermoPoblete/PGL

Software R package which links genetics and human brain imaging by using genes associated with disease and calculating normalized mRNA expression average of those genes in each brain region. By uploading lists of genes and brain regions of interest, this package will return csv with the results.

Proper citation: Process Genes List (RRID:SCR_023823) Copy   

•   Source: SciCrunch Registry

https://www.nitrc.org/projects/spm_mouse_toolb#

Software toolbox provides multi-modality murine image templates, all of which are spatially registered to the Allen Common Coordinate Framework. The images have been optimized for in-vivo preclinical imaging in terms of resolution and region-of-interest size. The ROIs have been derived from the Allen Brain Atlas. This image analysis tool can be used to facilitate the analysis of mouse PET-CT brain images.

Proper citation: PET-CT mouse brain toolbox (RRID:SCR_023821) Copy   

•   Source: SciCrunch Registry

http://www.loni.usc.edu/

Biomedical technology resource center specializing in novel approaches and tools for neuroimaging. It develops novel strategies to investigate brain structure and function in their full multidimensional complexity. There is a rapidly growing need for brain models comprehensive enough to represent brain structure and function as they change across time in large populations, in different disease states, across imaging modalities, across age and sex, and even across species. International networks of collaborators are provided with a diverse array of tools to create, analyze, visualize, and interact with models of the brain. A major focus of these collaborations is to develop four-dimensional brain models that track and analyze complex patterns of dynamically changing brain structure in development and disease, expanding investigations of brain structure-function relations to four dimensions.

Proper citation: Laboratory of Neuro Imaging (RRID:SCR_001922) Copy   

•   Source: SciCrunch Registry

https://ctsi.ucsf.edu

An institute which provides infrastructure, services, and training to support clinical and translational research. It develops broad coalitions and partnerships at the local and national levels to enable a transformation of the research environment.

Proper citation: UCSF Clinical and Translational Science Institute (RRID:SCR_014711) Copy   

•   Source: SciCrunch Registry