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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
http://carbonyldb.missouri.edu/CarbonylDB/index.php/
Curated data resource of protein carbonylation sites.Manually curated data resource of experimentally confirmed carbonylated proteins and sites.Provides information on other related resources such as list of other oxidative protein modification databases, list of protein oxidation and carbonylation prediction tools.
Proper citation: CarbonylDB (RRID:SCR_023924) Copy
Software for mouse colony management. Streamlined software for simplified colony management.
Proper citation: Transnetyx Colony Management (RRID:SCR_023922) Copy
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
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
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
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
https://github.com/ZhenjiangFan/DAG-deepVASE
Software tool for identifying nonlinear causal relations and estimating their effect size help to understand complex disease pathobiology.
Proper citation: DAG-deepVASE (RRID:SCR_023612) Copy
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
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
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
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
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
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
https://github.com/industrial-optimization-group/DESDEO
Software Python framework for interactive multiobjective optimization methods.
Proper citation: DESDEO (RRID:SCR_023502) Copy
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
Software application as medical image viewer.Able to load series of special images stored in DICOM format for review. Able to query and fetch DICOM images from archive nodes (also called PACS) over the network. Designed to run under Linux.
Proper citation: Aeskulap (RRID:SCR_023960) Copy
https://www.topazlabs.com/gigapixel-ai
Software to increase image resolution. Gigapixel AI’s neural networks are continuously trained on sample images to increase resolution of different subjects like portraits, wildlife, landscapes, architecture and image types like DSLR, web/compressed, CG.
Proper citation: Gigapixel AI (RRID:SCR_023684) Copy
https://github.com/PIEFoundry/Microfabrication/wiki/Parylene-MEA-Fabrication
Parylene MEA Fabrication is related to SPARC. Repository for standard fabrication procedure for Parylene C microelectrode arrays and similar devices.
Proper citation: HORNET CENTER FOR AUTONOMIC NERVE RECORDING AND STIMULATION SYSTEMS (RRID:SCR_023681) Copy
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
https://github.com/IBT-FMI/ABI-expression-data_generator
Software to download expression data from Allen Mouse Brain data portal ABI. This script will query database, download available data, convert it from the raw/mhd format to NIfTI, and register it to standard space. Package-manager-friendly archive of gene expression maps registered in SMRI standard space from the Allen Mouse Brain Atlas.
Proper citation: ABI-expression-data-generator (RRID:SCR_023834) Copy
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