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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.
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
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
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
https://github.com/statgen/Rprs
Software R package for computing Polygenic Risk Scores from dosages.
Proper citation: Rprs (RRID:SCR_023557) Copy
https://www.ebrains.eu/brain-atlases/analysis/gene-expression-analysis-in-human-brain-atlas-regions/
Software tool for integrating tissue transcriptome and cytoarchitectonic segregation. Combines data from Allen Human Brain Atlas and the EBRAINS Human Brain Atlas, specifically to discover how gene activities and microanatomical architectures contribute to brain function and dysfunction. Both tissue transcriptome and probabilistic brain segregation data allow for integrating genetic expression, brain structure, and function knowledge.
Proper citation: JuGEx (RRID:SCR_023838) Copy
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
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
https://github.com/petersaj/AP_histology
Software data pipeline which aligns histology images to the Allen CCF.
Proper citation: AP-histology (RRID:SCR_023847) Copy
Software tool that performs SET Operations including Set Intersections, Set Unions and Set Differences over lists of words, numbers etc with formatted results . Used for comparing differences between two lists.
Proper citation: ListDiff (RRID:SCR_023569) Copy
Software tool accurately classifies personal names by gender, country of origin or ethnicity. Can infer gender, translate Chinese names and Japanese names, format phone number, and split full name via user interface and API. Used as name checker for gender, origin and ethnicity determination.
Proper citation: NamSor (RRID:SCR_023935) Copy
https://github.com/AstraZeneca-NGS/VarDictJava
Software tool as variant caller for both single and paired sample variant calling from BAM files. Implements amplicon bias aware variant calling from targeted sequencing experiments, rescue of long indels by realigning bwa soft clipped reads.Novel and versatile variant caller for next generation sequencing in cancer research.
Proper citation: VarDict (RRID:SCR_023658) Copy
Software to correct spelling and grammar.
Proper citation: Grammarly (RRID:SCR_023778) Copy
https://www.chemcomp.com/Products.htm
Drug discovery platform to integrate visualization, modeling and simulation in single package. Integrated computer aided molecular design platform.
Proper citation: Molecular Operating Environment (RRID:SCR_023932) Copy
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