Initial commit

.Rbuildignore

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+^.*\.Rproj$
+^\.Rproj\.user$
+^LICENSE\.md$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^\.github$

.gitignore

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+docs
+inst/doc
+.Rproj.user
+.Rhistory
+.Rdata
+.httr-oauth
+.DS_Store

DESCRIPTION

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+Package: SCdeconR
+Type: Package
+Title: Deconvolution of bulk RNA-seq data using single-cell RNA-seq data as reference
+Version: 0.99.0
+Authors@R: person("Yuanhang", "Liu", email = "[email protected]", role = c("aut", "cre"))
+Description: Streamlined workflow from deconvolution of bulk RNA-seq data to downstream differential expression and gene-set enrichment analysis. Provide various visualization functions. 
+License: GPL (>= 3)
+URL: https://github.com/Liuy12/SCdeconR/,
+    https://liuy12.github.io/SCdeconR/
+Encoding: UTF-8
+LazyData: true
+RoxygenNote: 7.2.3
+Imports: 
+    data.table,
+    doFuture,
+    dplyr,
+    edgeR,
+    foreach,
+    future,
+    ggplot2,
+    gtools,
+    harmony,
+    MASS,
+    Matrix,
+    NMF,
+    Seurat
+Suggests: 
+    DESeq2,
+    FARDEEP,
+    knitr,
+    limma,
+    Linnorm,
+    MuSiC,
+    nnls,
+    plotly,
+    preprocessCore,
+    reticulate,
+    rmarkdown,
+    scater,
+    SCDC,
+    scran,
+    SingleCellExperiment,
+    spacexr,
+    xbioc
+Depends: 
+    R (>= 2.10)
+VignetteBuilder: knitr

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export(bulk_generator)
+export(celltype_expression)
+export(comparedeg_scatter)
+export(comparegsea_scatter)
+export(compute_metrics)
+export(construct_ref)
+export(gsea_heatmap)
+export(gsea_rwplot)
+export(gsea_sumplot)
+export(load_scdata)
+export(prepare_rnk)
+export(prop_barplot)
+export(read_gmt)
+export(reformat_gmt)
+export(run_de)
+export(scaling)
+export(scdecon)
+export(transformation)
+export(write_gmt)
+importFrom(MASS,rlm)
+importFrom(Matrix,colSums)
+importFrom(Matrix,rowMeans)
+importFrom(Matrix,rowSums)
+importFrom(NMF,aheatmap)
+importFrom(data.table,fread)
+importFrom(data.table,fwrite)
+importFrom(gtools,mixedsort)
+importFrom(reshape2,dcast)
+importFrom(reshape2,melt)

NEWS.md

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+# SCdeconR 0.99.0
+
+* Pre-release version

R/SCdeconR-package.R

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+#' @keywords internal
+"_PACKAGE"
+
+## usethis namespace: start
+#' @importFrom MASS rlm
+#' @importFrom Matrix rowMeans
+#' @importFrom Matrix rowSums
+#' @importFrom Matrix colSums
+#' @importFrom NMF aheatmap
+#' @importFrom data.table fread
+#' @importFrom data.table fwrite
+#' @importFrom gtools mixedsort
+#' @importFrom reshape2 dcast
+#' @importFrom reshape2 melt
+## usethis namespace: end
+NULL

R/data.R

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+#' Integrated scRNA-seq reference for breast tissue (subset)
+#' 
+#' Integrated scRNA-seq reference using random subset of two scRNA-seq datasets for breast tissue. One sample is from Komen tissue bank. 
+#' The other sample is from Gtex snRNA-seq data.
+#' 
+#' @format `refdata`
+#' a \code{\link[Seurat]{Seurat-class}} object with several metadata included:
+#' \describe{
+#'  \item{cellid}{cell barcodes}
+#'  \item{celltypes}{annotated cell types}
+#'  \item{subjectid}{subject id}
+#'  \item{cohort}{data cohort, either "komentissuebank" or "gtex"}
+#' }
+#' 
+#' @source 
+#' <https://gtexportal.org/home/singleCellOverviewPage>
+#' <A single-cell atlas of the healthy breast tissues reveals clinically relevant clusters of breast epithelial cells>
+"refdata"