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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://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.juntadeandalucia.es/fundacionprogresoysalud/es/home

An organization that supports the public health system in Andalusia, Spain through three main activities: research and innovation in health, technologies line information and communication, and training and evaluation of professional skills. It also provides management support to the Health Quality Agency of Andalusia, which is the driving entity of the Andalusian Quality Model. Resource is in Spanish.

Proper citation: Progress and Health Foundation; Seville; Spain (RRID:SCR_000276) Copy   

•   Source: SciCrunch Registry

http://hadoop.apache.org/

Software library providing a framework that allows for the distributed processing of large data sets across clusters of computers using simple programming models. It is designed to scale up from single servers to thousands of machines, each offering local computation and storage. Rather than rely on hardware to deliver high-availability, the library itself is designed to detect and handle failures at the application layer, so delivering a highly-available service on top of a cluster of computers, each of which may be prone to failures. The project includes these modules: * Hadoop Common: The common utilities that support the other Hadoop modules. * Hadoop Distributed File System (HDFS): A distributed file system that provides high-throughput access to application data. * Hadoop YARN: A framework for job scheduling and cluster resource management. * Hadoop MapReduce: A YARN-based system for parallel processing of large data sets.

Proper citation: Apache Hadoop (RRID:SCR_011879) Copy   

•   Source: SciCrunch Registry

http://nemo.nic.uoregon.edu/wiki/NEMO_Analysis_Toolkit

THIS RESOURCE IS NO LONGER IN SERVICE. NIH tombstone webpage lists Project Period : 2009 - 2013. The NEMO ERP Analysis Toolkit includes tools for EEG/ERP and MEG data decomposition, and ontology-based mark-up, annotation, and labeling of patterns in EEG and MEG data. These tools have been implemented in MATLAB by Robert Frank, a mathematician and data analyst for NEMO. The current NEMO analysis pipeline has been designed with the aim to support cross-lab, cross-experiment meta-analysis of EEG and MEG data. The current proposed processing pipeline consists of the following steps: * Step 1: Decomposing ERP data (continuous data are transformed into discrete patterns for analysis) o PCA/ ICA/Microstate * Step 2: Marking up the analysis results o Each pattern is annotated with labels that relate pattern attributes to NEMO ontology concepts * Step 3: Clustering the observed patterns within and across experimental groups * Step 4: Labeling the cross-experiment clusters Each item in the above list is a step/phase in the processing pipeline and is associated with a set of matlab scripts in our NEMO ERP Analysis Toolkit, which is implemented by a collection of MATLAB scripts.

Proper citation: NEMO Analysis Toolkit (RRID:SCR_013624) Copy   

•   Source: SciCrunch Registry

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

Software R package. Methods for Cluster analysis. Performs variety of types of cluster analysis and other types of processing on large microarray datasets.

Proper citation: Cluster (RRID:SCR_013505) Copy   

•   Source: SciCrunch Registry

https://github.com/MicrosoftGenomics/FaST-LMM

FaST-LMM (Factored Spectrally Transformed Linear Mixed Models) is a set of tools for efficiently performing genome-wide association studies (GWAS), prediction, and heritability estimation on large data sets.

Proper citation: FaST LMM (RRID:SCR_015506) Copy   

•   Source: SciCrunch Registry