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")):
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("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 | ||
| LICENSE | Text |
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) | augere.solo_0.99.3.zip |
| macOS Binary (big-sur-x86_64) | augere.solo_0.99.3.tgz |
| macOS Binary (sonoma-arm64) | augere.solo_0.99.3.tgz |
| 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 |