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DeconvoBuddies

This is the development version of DeconvoBuddies; to use it, please install the devel version of Bioconductor.

Helper Functions for LIBD Deconvolution


Bioconductor version: Development (3.21)

Funtions 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] ORCID iD ORCID: 0000-0001-5148-3602 , Leonardo Collado-Torres [ctb] ORCID iD ORCID: 0000-0003-2140-308X

Maintainer: Louise Huuki-Myers <lahuuki at gmail.com>

Citation (from within R, enter citation("DeconvoBuddies")):

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 PDF
NEWS Text

Details

biocViews ExperimentHubSoftware, GeneExpression, RNASeq, SingleCell, Software, Transcriptomics
Version 0.99.39
In Bioconductor since BioC 3.21 (R-4.5)
License Artistic-2.0
Depends R (>= 4.4.0)
Imports AnnotationHub, BiocFileCache, dplyr, ExperimentHub, ggplot2, graphics, grDevices, matrixStats, methods, purrr, rafalib, reshape2, S4Vectors, scran, SingleCellExperiment, spatialLIBD, stats, stringr, SummarizedExperiment, tibble, utils
System Requirements
URL https://github.com/lahuuki/DeconvoBuddies
Bug Reports https://github.com/LieberInstitute/DeconvoBuddies/issues
See More
Suggests Biobase, BiocStyle, BisqueRNA, covr, HDF5Array, knitr, RColorBrewer, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0), tidyr, tidyverse
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package DeconvoBuddies_0.99.39.tar.gz
Windows Binary (x86_64) DeconvoBuddies_0.99.39.zip
macOS Binary (x86_64) DeconvoBuddies_0.99.39.tgz
macOS Binary (arm64) DeconvoBuddies_0.99.39.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