augere.solo
This is the development version of augere.solo; to use it, please install the devel version of Bioconductor.
Automatic Generation of Single-Cell Analyses
Bioconductor version: Development (3.24)
Implements pipelines for generating single-cell analysis reports in the augere framework. This uses scrapper to execute routine steps such as quality control, normalization, feature selection, clustering and marker detection. We also implement a pipeline for automatic cell type annotation against a labelled reference with SingleR. Each pipeline function generates a self-contained Rmarkdown report with all of the steps required to reproduce its analysis.
Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>
citation("augere.solo")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("augere.solo")
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("augere.solo")| Simple single-cell analyses | HTML | R Script |
| Reference Manual |
Details
| biocViews | ReportWriting, SingleCell, Software, WorkflowManagement |
| Version | 0.99.3 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | |
| Imports | augere.core, scrapper, scater |
| System Requirements | |
| URL | https://github.com/augere-bioinfo/augere.solo |
| Bug Reports | https://github.com/augere-bioinfo/augere.solo/issues |
See More
| Suggests | testthat, knitr, rmarkdown, BiocStyle, BiocGenerics, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment, SingleCellExperiment, scRNAseq, SingleR, celldex, jsonlite |
| 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 | augere.solo_0.99.3.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (big-sur-arm64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/augere.solo |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/augere.solo |
| Bioc Package Browser | https://code.bioconductor.org/browse/augere.solo/ |
| Package Short Url | https://bioconductor.org/packages/augere.solo/ |
| Package Downloads Report | Download Stats |