HuBMAPR
This is the development version of HuBMAPR; for the stable release version, see HuBMAPR.
Interface to 'HuBMAP'
Bioconductor version: Development (3.24)
'HuBMAP' provides an open, global bio-molecular atlas of the human body at the cellular level. The `datasets()`, `samples()`, `donors()`, `publications()`, and `collections()` functions retrieves the information for each of these entity types. `*_details()` are available for individual entries of each entity type. `*_derived()` are available for retrieving derived datasets or samples for individual entries of each entity type. Data files can be accessed using `bulk_data_transfer()`.
Author: Christine Hou [aut, cre]
, Martin Morgan [aut]
, Federico Marini [aut]
Maintainer: Christine Hou <chris2018hou at gmail.com>
citation("HuBMAPR")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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("HuBMAPR")
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("HuBMAPR")| Accessing Human Cell Atlas Data | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataImport, Infrastructure, SingleCell, Software, Spatial, ThirdPartyClient |
| Version | 1.7.2 |
| In Bioconductor since | BioC 3.20 (R-4.4) (2 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.4.0) |
| Imports | httr2, dplyr, tidyr, tibble, rjsoncons, utils, stringr, whisker, purrr, rlang |
| System Requirements | |
| URL | https://christinehou11.github.io/HuBMAPR/ https://github.com/christinehou11/HuBMAPR |
| Bug Reports | https://github.com/christinehou11/HuBMAPR/issues |
See More
| Suggests | testthat (>= 3.0.0), knitr, ggplot2, rmarkdown, BiocStyle, lobstr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | HuBMAPR_1.7.2.tar.gz |
| Windows Binary (x86_64) | HuBMAPR_1.7.2.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | HuBMAPR_1.7.2.tgz |
| macOS Binary (sonoma-arm64) | HuBMAPR_1.7.2.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/HuBMAPR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/HuBMAPR |
| Bioc Package Browser | https://code.bioconductor.org/browse/HuBMAPR/ |
| Package Short Url | https://bioconductor.org/packages/HuBMAPR/ |
| Package Downloads Report | Download Stats |