Awesome Rpackages

Single cell

Doublet

• DoubletCollection R package that integrates the installation, execution and benchmark of eight cutting-edge computational doublet-detection methods.

batch integration

• scMerge R package for merging and normalising single-cell RNA-Seq datasets.

preprocessing

• scCancer a package for automated processing of single-cell RNA-seq data in cancer

cell type annotation

• scATOMIC Single Cell Annotation of TumOur Microenvironments In pan-Cancer
• scAnno An automated annotation tool for single-cell RNA sequencing datasets primarily based on the single cell cluster levels, using a joint deconvolution strategy and logistic regression

Infer malignant cells

• infercna Infer Copy Number Alterations and Clonality in (Single-Cell) RNA-Seq Data

funtional enrichment

• escape Easy single cell analysis platform for enrichment

meta program

• GeneNMF unsupervised discovery of gene programs in single-cell data

object convert

• schard This package allows one to load scanpy h5ad into R as list, SingleCellExperiment or Seurat object. For now it only loads X, obs, var, obsm (as reduced dimensions) if requested and images for visium data. The package is based on rhdf5 for h5ad manipulation and is pure R (that is reticulate-free).

Stats

• easystats An R Framework for Easy Statistical Modeling, Visualization, and Reporting

Data Manipulation

• tidyfst A toolkit of tidy data manipulation verbs with data.table as the backend

Visualization

• bbplot A theme pakage with BBC News
• webr Plot for distribution of statistic and p-value
• ggkegg A set of functions to analyse and plot the KEGG information