Package: DeconvoBuddies 1.4.0

Louise Huuki-Myers

DeconvoBuddies: Helper Functions for LIBD Deconvolution

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.

Authors:Louise Huuki-Myers [aut, cre], Leonardo Collado-Torres [ctb], Nicholas J. Eagles [ctb]

DeconvoBuddies_1.4.0.tar.gz
DeconvoBuddies_1.4.0.zip(r-4.7)DeconvoBuddies_1.4.0.zip(r-4.6)DeconvoBuddies_1.4.0.zip(r-4.5)
DeconvoBuddies_1.4.0.tgz(r-4.6-any)DeconvoBuddies_1.4.0.tgz(r-4.5-any)
DeconvoBuddies_1.4.0.tar.gz(r-4.7-any)DeconvoBuddies_1.4.0.tar.gz(r-4.6-any)
DeconvoBuddies_1.4.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
DeconvoBuddies/json (API)
NEWS

# Install 'DeconvoBuddies' in R:

install.packages('DeconvoBuddies', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/lieberinstitute/deconvobuddies/issues

Datasets:

est_prop - Bisque Estimated Cell Type Proportions for DLPFC bulk RNA-seq data
est_prop_test - Test Estimated Cell Type Proportions
marker_stats_1vAll - 1vAll Marker Statistics example data
marker_test - Markers stats from sce_DLPFC_example
RNAScope_prop - Cell Type Proportions estimated from RNAScope
rse_bulk_test - Test bulk rse dataset
sce_ab - Toy SCE object for testing

On BioConductor:DeconvoBuddies-1.5.0(bioc 3.24)DeconvoBuddies-1.4.0(bioc 3.23)

software singlecell rnaseq geneexpression transcriptomics experimenthubsoftware bioconductor deconvolution

7.47 score 10 stars 49 scripts 273 downloads 10 exports 197 dependencies

Last updated from:f117cdae8a (on RELEASE_3_23). Checks:8 WARNING, 2 OK. Indexed: no.

Target	Result	Time
bioc-checks	WARNING	299
linux-devel-x86_64	WARNING	621
source / vignettes	OK	1151
linux-release-x86_64	WARNING	596
macos-release-arm64	WARNING	617
macos-oldrel-arm64	WARNING	549
windows-devel	WARNING	1052
windows-release	WARNING	1344
windows-oldrel	WARNING	1077
wasm-release	OK	259

Exports:create_cell_colors fetch_deconvo_data findMarkers_1vAll get_mean_ratio make_test_sce plot_composition_bar plot_gene_express plot_marker_express plot_marker_express_ALL plot_marker_express_List

Dependencies:abind AnnotationDbi AnnotationHub askpass assorthead attempt base64enc beachmat beeswarm benchmarkme benchmarkmeData BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocManager BiocNeighbors BiocParallel BiocSingular BiocVersion Biostrings bit bit64 bitops blob bluster bslib cachem Cairo cigarillo circlize cli clue cluster codetools colorspace commonmark ComplexHeatmap config cowplot cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray DelayedMatrixStats digest doParallel dplyr dqrng DT edgeR evaluate ExperimentHub farver fastmap filelock FNN fontawesome foreach formatR fs futile.logger futile.options generics GenomicAlignments GenomicRanges GetoptLong ggbeeswarm ggplot2 ggrastr ggrepel GlobalOptions glue golem gridExtra gtable here highr htmltools htmlwidgets httpuv httr httr2 igraph IRanges irlba isoband iterators jquerylib jsonlite KEGGREST knitr labeling lambda.r later lattice lazyeval lifecycle limma locfit magick magrittr Matrix MatrixGenerics matrixStats memoise metapod mime openssl otel paletteer pheatmap pillar pkgconfig plotly plyr png prismatic promises purrr R6 rafalib ragg rappdirs RColorBrewer Rcpp RcppAnnoy RcppEigen RcppML RcppProgress RCurl rematch2 reshape2 restfulr Rhtslib rjson rlang rmarkdown rprojroot Rsamtools RSpectra RSQLite rstudioapi rsvd rtracklayer Rtsne S4Arrays S4Vectors S7 sass ScaledMatrix scales scater scran scuttle Seqinfo sessioninfo shape shiny shinyWidgets SingleCellExperiment sitmo snow sourcetools SparseArray sparseMatrixStats SpatialExperiment spatialLIBD statmod stringi stringr SummarizedExperiment sys systemfonts textshaping tibble tidyr tidyselect tinytex utf8 uwot vctrs vipor viridis viridisLite withr xfun XML xtable XVector yaml

Deconvolution Benchmark in Human DLPFC

Louise Huuki-Myers

Rendered fromDeconvolution_Benchmark_DLPFC.Rmdusingknitr::rmarkdownon Jun 11 2026.

Last update: 2025-07-28
Started: 2024-03-27

Finding Marker Genes with DeconvoBuddies

Louise Huuki-Myers

Rendered fromMarker_Finding.Rmdusingknitr::rmarkdownon Jun 11 2026.

Last update: 2026-03-03
Started: 2024-08-05

Get Started with DeconvoBuddies

Louise Huuki-Myers

Rendered fromDeconvoBuddies.Rmdusingknitr::rmarkdownon Jun 11 2026.

Last update: 2025-07-25
Started: 2021-11-30

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Create a cell color palette for plots	create_cell_colors
Bisque Estimated Cell Type Proportions for DLPFC bulk RNA-seq data	est_prop
Test Estimated Cell Type Proportions	est_prop_test
Download Human DLPFC Deconvolution Data	fetch_deconvo_data
Calculate 1 vs. All standard fold change for each gene x cell type, wrapper function for 'scran::findMarkers()'.	findMarkers_1vAll
Get Mean Ratio for Each Gene x Cell Type	get_mean_ratio
Simulate a SingleCellExperiment for testing.	make_test_sce
1vAll Marker Statistics example data	marker_stats_1vAll
Markers stats from sce_DLPFC_example	marker_test
Create barplot of average cell type composition	plot_composition_bar
Plot the gene expression of a list of genes in a SCE object	plot_gene_express
Plot gene expression violin plots for top marker genes for one cell type	plot_marker_express
Plot the top marker genes for ALL cell types	plot_marker_express_ALL
Plot a nested list of genes as a multi-page pdf	plot_marker_express_List
Cell Type Proportions estimated from RNAScope	RNAScope_prop
Test bulk rse dataset	rse_bulk_test
Toy SCE object for testing	sce_ab

Package: DeconvoBuddies 1.4.0

DeconvoBuddies: Helper Functions for LIBD Deconvolution

Deconvolution Benchmark in Human DLPFC

Finding Marker Genes with DeconvoBuddies

Get Started with DeconvoBuddies

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)