HTAN
This is the development version of HTAN; to use it, please install the devel version of Bioconductor.
Query and Retrieve Human Tumor Atlas Network (HTAN) Open-Access Data
Bioconductor version: Development (3.24)
A client for the open-access data of the Human Tumor Atlas Network (HTAN), Phase 1. File, biospecimen, clinical and provenance metadata are queried locally from a versioned parquet snapshot of the ISB-CGC HTAN BigQuery release tables, through DuckDB and dbplyr, with no Google account. Open-access files are downloaded from the CRDC General Commons (anonymous GA4GH DRS) or Synapse (personal access token), and common HTAN file formats are read into Bioconductor classes such as SingleCellExperiment, SpatialExperiment and MultiAssayExperiment.
Author: Sean Davis [aut, cre] 
, National Cancer Institute [fnd] (Grant U24CA289073)
Maintainer: Sean Davis <seandavi at gmail.com>
citation("HTAN")):Sean Davis. HTAN: Query and Retrieve Human Tumor Atlas Network (HTAN) Open-Access Data. doi:10.18129/B9.bioc.HTAN, R package version 0.99.1, https://bioconductor.org/packages/HTAN.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("HTAN")For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("HTAN")| analysis-workflow.html | HTML | R Script |
| atlas-overview.html | HTML | R Script |
| data-model.html | HTML | R Script |
| HTAN.html | HTML | R Script |
| Reference Manual |
Details
| biocViews | BiomedicalInformatics, DataImport, DataRepresentation, SingleCell, Software, Spatial, ThirdPartyClient, Transcriptomics |
| Version | 0.99.1 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.5.0) |
| Imports | BiocFileCache, DBI, dbplyr, dplyr, duckdb, httr2, jsonlite, methods, MultiAssayExperiment, rlang, S4Vectors, SingleCellExperiment, SpatialExperiment, stats, SummarizedExperiment, tibble, tools, utils |
| System Requirements | Quarto command line tool (<https://github.com/quarto-dev/quarto-cli>). |
| URL | https://github.com/seandavi/HTAN https://seandavi.github.io/HTAN/ |
| Bug Reports | https://github.com/seandavi/HTAN/issues |
See More
| Suggests | anndataR, BiocIO, ggplot2, knitr, Matrix, quarto, rhdf5, scales, scater, scrapper, SeuratObject, TENxIO, tidyr, testthat (>= 3.0.0), VisiumIO, withr |
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| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | HTAN_0.99.1.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/HTAN |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/HTAN |
| Package Short Url | https://bioconductor.org/packages/HTAN/ |
| Package Downloads Report | Download Stats |