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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://www.transnetyx.com/colony?gad=1&gclid=CjwKCAjw8symBhAqEiwAaTA__GhOxQovqufxibmOSyRqtSo__-EMrnF9OGpdOAvAPgUOTE47h8TONBoCyMMQAvD_BwE

Software for mouse colony management. Streamlined software for simplified colony management.

Proper citation: Transnetyx Colony Management (RRID:SCR_023922) Copy   

•   Source: SciCrunch Registry

https://github.com/wkusmirek/mONiTor

Software tool monitors metrics available in sequencer, state of the computer to which the sequencer is connected, and the contents of the fast5 and fastq files. Real-time monitoring of Oxford Nanopore Technology sequencing run. Used for monitoring nanopore sequencing process.

Proper citation: mONiTor (RRID:SCR_023921) Copy   

•   Source: SciCrunch Registry

http://statbio.github.io/Sargasso/

Software Python tool to disambiguate mixed species RNA-seq reads according to their species of origin.

Proper citation: Sargasso (RRID:SCR_023489) Copy   

•   Source: SciCrunch Registry

https://ginkgo-cadx.com/en/

Software advanced DICOM viewer and dicomizer that can also be used to convert png, jpeg, bmp, pdf, tiff to DICOM files.

Proper citation: Ginkgo CADx (RRID:SCR_024031) Copy   

•   Source: SciCrunch Registry

http://samtools.github.io/htsjdk/

Software implementation of unified Java library for accessing common file formats, such as SAM and VCF, used for high-throughput sequencing data. There are also an number of useful utilities for manipulating HTS data.

Proper citation: HTSJDK (RRID:SCR_024036) Copy   

•   Source: SciCrunch Registry

http://proteomics.ucsd.edu/Software/Inspect/

Software tool to addresses several algorithmic problems in order to identify modified proteins.Software MS/MS database search tool specifically designed to address two crucial needs of the proteomics comminuty: post-translational modification identification and search speed.

Proper citation: InsPecT (RRID:SCR_024038) 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/brainglobe/brainreg

Software Python based tool that registers the template brain (e.g. from the Allen Reference Atlas) to the sample image.Automated 3D brain registration with support for multiple species and atlases.

Proper citation: Brainreg (RRID:SCR_023858) 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://bibus-biblio.sourceforge.net/

Bibliographic and reference management software. Allows to search, edit, and sort bibliographic records.

Proper citation: Bibus (RRID:SCR_023974) 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/klebgenomics/Kaptive

Software tool to report information about surface polysaccharide loci for Klebsiella pneumoniae species complex and Acinetobacter baumannii genome assemblies.

Proper citation: Kaptive (RRID:SCR_024046) Copy   

•   Source: SciCrunch Registry

https://www.jabref.org/

Open source, software cross platform citation and reference management tool.Helps to collect and organize sources, find the paper, discover the latest research.

Proper citation: JabRef (RRID:SCR_024047) Copy   

•   Source: SciCrunch Registry

https://userbase.kde.org/KBibTeX

Software tool as bibliography editor for KDE. Used in conjunction with Kile. BibTeX editor for KDE. KBibTeX's primary file format is BibTeX as known from LaTeX, but other formats such as RIS, PDF, or RTF can be imported and exported.

Proper citation: KBibTeX (RRID:SCR_024048) Copy   

•   Source: SciCrunch Registry

https://www.microsoft.com/en-my/microsoft-365/powerpoint

Presentation software developed by Microsoft Corporation. Part of Microsoft Office suite. Used for creating slideshows and delivering presentations.

Proper citation: Microsoft PowerPoint (RRID:SCR_023631) 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://zonationteam.github.io/Zonation5/

Spatial prioritization software used to identify priority areas to support conservation planning, land use planning, ecological impact avoidance and other similar tasks.

Proper citation: Zonation 5 (RRID:SCR_023745) 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