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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://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://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
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/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://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://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
Artificial Iinteligence chatbot that uses natural language processing to create humanlike conversational dialogue. Notable for enabling users to refine and steer conversation towards desired length, format, style, level of detail, and language used. Sibling model to InstructGPT, which is trained to follow instruction in prompt and provide detailed response.
Proper citation: ChatGPT (RRID:SCR_023775) Copy
https://github.com/singleron-RD/CeleScope
Software tool as collection of bioinfomatics analysis pipelines to process single cell sequencing data generated with Singleron products. Single cell analysis pipelines developed by Singleron Biotechnologies.
Proper citation: CeleScope (RRID:SCR_023553) Copy
https://github.com/churchmanlab/genewalk
Software for individual genes functions determination that are relevant in particular biological context and experimental condition. Quantifies similarity between vector representations of gene and annotated GO terms through representation learning with random walks on condition specific gene regulatory network. Similarity significance is determined through comparison with node similarities from randomized networks.
Proper citation: GeneWalk (RRID:SCR_023787) Copy
https://github.com/biod/sambamba
Software tool to filter SAM file for soft and hard clipped alignments
Proper citation: samclip (RRID:SCR_024330) Copy
https://github.com/ekg/seqwish
Software tool for alignment to variation graph inducer.
Proper citation: seqwish (RRID:SCR_024332) Copy
https://metacpan.org/dist/Bio-Chado-Schema
Standard object-relational mapping layer for use with GMOD Chado database schema. This layer is implemented with DBIx::Class, generated with the help of DBIx::Class::Schema::Loader module.
Proper citation: Bio-Chado-Schema (RRID:SCR_024059) Copy
https://github.com/cbrnr/sigviewer
Software viewing application for biosignals such as EEG or MEG time series. In addition to viewing raw data, SigViewer can also create, edit, and display event information such as annotations or artifact selections.
Proper citation: sigviewer (RRID:SCR_024340) Copy
Open source Python-based optimization modeling language with diverse set of optimization capabilities.
Proper citation: pyomo (RRID:SCR_024188) Copy
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