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Open Source Science

https://github.com/christinehou11/humanhippocampus2024

Access to spatial HPC project data

https://github.com/christinehou11/humanhippocampus2024

Science Score: 13.0%

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    Low similarity (9.2%) to scientific vocabulary

Keywords

bioconductor-package database experimenthub single-nucleus-rna-sequencing spatial-transcriptomics
Last synced: 5 months ago · JSON representation

Repository

Access to spatial HPC project data

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bioconductor-package database experimenthub single-nucleus-rna-sequencing spatial-transcriptomics
Created over 1 year ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog Contributing Code of conduct Support

README.md

humanHippocampus2024

Lifecycle: experimental check-bioc Codecov test coverage

Welcome to the humanHippocampus2024 package!

This package helps to access the spatially-resolved transcriptomics (SRT) and single-nucleus RNA-sequencing (snRNA-seq) data from adjacent tissue sections of the anterior human hippocampus across ten adult neurotypical donors generated by Lieber Institute for Brain Development (LIBD) researchers and collaborators.

Installation

Please use R (version "4.4") and Bioconductor 3.20 then enter:

``` r if (!requireNamespace("BiocManager", quietly = TRUE)) { install.packages("BiocManager") }

BiocManager::install("humanHippocampus2024")

Check that you have a valid Bioconductor installation

BiocManager::valid() ```

The development version can be installed from GitHub:

r install.packages("remotes") remotes::install_github("christinehou11/humanHippocampus2024")

Please read Introduction to humanHippocampus2024 for detailed descriptions and tutorials.

Data Specifics

  • spe.rda: (spe object) SpatialExperiment with spatially-resolved transcriptomics (SRT) from adjacent tissue sections of the anterior human hippocampus across ten adult neurotypical donors usng 10x Genomics Visium, generated at the Lieber Institute for Brain Development (LIBD)

  • sce.rda: (sce object) SingleCellExperiment with single-nucleus RNA-sequencing (snRNA-seq) from adjacent tissue sections of the anterior human hippocampus across ten adult neurotypical donors usng 10x Genomics Visium, generated at the Lieber Institute for Brain Development (LIBD)

Code of Conduct

Please note that the humanHippocampus2024 project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

Owner

  • Login: christinehou11
  • Kind: user

GitHub Events

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  • Push event: 11
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Last Year
  • Push event: 11
  • Create event: 1

Dependencies

.github/workflows/check-bioc.yml actions
  • JamesIves/github-pages-deploy-action releases/v4 composite
  • actions/cache v3 composite
  • actions/checkout v3 composite
  • actions/upload-artifact master composite
  • docker/build-push-action v4 composite
  • docker/login-action v2 composite
  • docker/setup-buildx-action v2 composite
  • docker/setup-qemu-action v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
DESCRIPTION cran
  • R >= 4.4 depends
  • AnnotationHubData * suggests
  • BiocStyle * suggests
  • ExperimentHub * suggests
  • RefManageR * suggests
  • SpatialExperiment * suggests
  • SummarizedExperiment * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • sessioninfo * suggests
  • testthat >= 3.0.0 suggests