DeconvoBuddies
This is the released version of DeconvoBuddies; for the devel version, see DeconvoBuddies.
Helper Functions for LIBD Deconvolution
Bioconductor version: Release (3.23)
Functions helpful for LIBD deconvolution project. Includes tools for marker finding with mean ratio, expression plotting, and plotting deconvolution results. Working to include DLPFC datasets.
Author: Louise Huuki-Myers [aut, cre]
, Leonardo Collado-Torres [ctb]
, Nicholas J. Eagles [ctb]
Maintainer: Louise Huuki-Myers <lahuuki at gmail.com>
citation("DeconvoBuddies")):
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")
BiocManager::install("DeconvoBuddies")
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("DeconvoBuddies")| Deconvolution Benchmark in Human DLPFC | HTML | R Script |
| Finding Marker Genes with DeconvoBuddies | HTML | R Script |
| Get Started with DeconvoBuddies | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ExperimentHubSoftware, GeneExpression, RNASeq, SingleCell, Software, Transcriptomics |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.21 (R-4.5) (1.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.4.0) |
| Imports | AnnotationHub, BiocFileCache, BiocParallel, DelayedMatrixStats, dplyr, ExperimentHub, ggplot2, ggrepel, graphics, grDevices, MatrixGenerics, methods, purrr, rafalib, reshape2, S4Vectors, scran, SingleCellExperiment, spatialLIBD, stats, stringr, SummarizedExperiment, tibble, utils |
| System Requirements | |
| URL | https://github.com/LieberInstitute/DeconvoBuddies |
| Bug Reports | https://github.com/LieberInstitute/DeconvoBuddies/issues |
See More
| Suggests | Biobase, BiocStyle, covr, HDF5Array, knitr, RColorBrewer, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0), tidyr, tidyverse |
| 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 | DeconvoBuddies_1.4.0.tar.gz |
| Windows Binary (x86_64) | DeconvoBuddies_1.4.0.zip |
| macOS Binary (big-sur-x86_64) | DeconvoBuddies_1.4.0.tgz |
| macOS Binary (sonoma-arm64) | DeconvoBuddies_1.4.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/DeconvoBuddies |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/DeconvoBuddies |
| Bioc Package Browser | https://code.bioconductor.org/browse/DeconvoBuddies/ |
| Package Short Url | https://bioconductor.org/packages/DeconvoBuddies/ |
| Package Downloads Report | Download Stats |