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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://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://blimp.cs.queensu.ca/

Bibliography covering all publications related to the fast-growing field of biomedical literature and text mining. This forum for collecting, compiling and sharing is a one-stop resource, letting researchers find out who-does-what in the area and where it is published, bridging across the many discipline-specific venues in which biomedical text-mining papers are published. If you know of a relevant paper that is missing from BLIMP, or have an accepted-for-publication paper, PhD/MSc thesis or a technical report, that you believe is relevant to biomedical text mining, fill in the submission form. The fast-growing field of biomedical literature mining is highly-interdisciplinary. Publications appear in forums ranging from the SIGIR conferences (the ACM Special Interest group on Information Retrieval) to journals such as Nature and Science, with the whole range of bioinformatics forums in-between. To substantially contribute, one must know what was/is being done in this diverse area, and place the work in context - both biologically and computationally. Instead of starting a journal fully dedicated to biomedical literature mining, thus creating yet another publication venue, this site offers an alternative: It holds in one place a compilation of references to relevant papers that have been published or accepted for publication.

Proper citation: BLIMP: Biomedical LIterature Mining Publications (RRID:SCR_007112) Copy   

•   Source: SciCrunch Registry

https://www.bio-rad.com/en-us/product/ze5-cell-analyzer?ID=OC62Q015

BioRad ZE5 was formerly known as the Propel Labs YETI Cytometer with configurations to meet broad range of experimental complexities and throughput needs. Accessible for novice flow cytometry users yet flexible enough for most experienced flow cytometry professionals.

Proper citation: Bio-Rad: ZE5 Cell Analyzer (RRID:SCR_019712) Copy   

•   Source: SciCrunch Registry

https://timothyspringer.org/files/tas/files/biacore3000-instrument.pdf

Biacore 3000 processing unit is an established, label-free system for detailed studies of biomolecular interactions. The system delivers comprehensive characterization of the interaction, answers questions about the rate constants, affinity, specificity, and determines the active concentration of components. The ability to recover and transfer interaction partners directly to MALDI targets for identification and further characterization makes the system highly applicable to fast identification of unknown interactants.

Proper citation: GE: Biacore 3000 Real Time Biomolecular Interaction Analyzer (RRID:SCR_018044) Copy   

•   Source: SciCrunch Registry

http://www.ou.edu/

A coeducational public research university located in Oklahoma, USA. The institution confers undergraduate and graduate degrees in fields such as law, medicine, aviation, energy management, history of science, and Native American studies.

Proper citation: University of Oklahoma; Oklahoma; USA (RRID:SCR_001074) Copy   

•   Source: SciCrunch Registry