DeconvoBuddies

This is the released version of DeconvoBuddies; for the devel version, see DeconvoBuddies.

Helper Functions for LIBD Deconvolution

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DOI: 10.18129/B9.bioc.DeconvoBuddies

Bioconductor version: Release (3.22)

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")
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews ExperimentHubSoftware, GeneExpression, RNASeq, SingleCell, Software, Transcriptomics

Version 1.2.0

In Bioconductor since BioC 3.21 (R-4.5) (0.5 years)

License Artistic-2.0

Depends R (>= 4.4.0)

Imports AnnotationHub, BiocFileCache, DelayedMatrixStats, dplyr, ExperimentHub, ggplot2, graphics, grDevices, MatrixGenerics, 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

Suggests Biobase, BiocStyle, 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_1.2.0.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64) DeconvoBuddies_1.2.0.tgz

macOS Binary (arm64) DeconvoBuddies_1.2.0.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/

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