scProkaR
This is the development version of scProkaR; to use it, please install the devel version of Bioconductor.
Microbial Single-Cell RNA-Seq Analysis for Bacterial Systems
Bioconductor version: Development (3.24)
scProkaR provides a SingleCellExperiment-centred workflow for microbial single-cell RNA sequencing data. It standardises bacterial input objects from count matrices, 10x Genomics directories or Seurat objects, and computes prokaryote-specific quality-control metrics such as ribosomal RNA fraction. It performs batch integration with several backends and scores the resulting embeddings with scIB-inspired benchmarking metrics. It also supports pseudobulk differential expression with edgeR and Time Aware Trajectory Analysis (TATA), a time-informed trajectory abstraction for perturbation time courses.
Author: Jinxin Zhao [aut, cre] 
, Ning Liu [aut], Alexander von Humboldt Foundation [fnd] (Fellowship support for Jinxin Zhao)
Maintainer: Jinxin Zhao <jinxin.zhao at monash.edu>
citation("scProkaR")):Jinxin Zhao, Ning Liu. scProkaR: Microbial Single-Cell RNA-Seq Analysis for Bacterial Systems. doi:10.18129/B9.bioc.scProkaR, R package version 0.99.3, https://bioconductor.org/packages/scProkaR.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("scProkaR")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("scProkaR")| scProkaR core workflow for microbial single-cell RNA-seq | HTML |
| Time Aware Trajectory Analysis (TATA) with scProkaR | HTML |
| Reference Manual | |
| NEWS | Text |
Details
| biocViews | BatchEffect, Clustering, DifferentialExpression, DimensionReduction, GeneExpression, GraphAndNetwork, Microbiome, MultipleComparison, Normalization, QualityControl, RNASeq, Sequencing, SingleCell, Software, TimeCourse, Transcriptomics, Visualization |
| Version | 0.99.3 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.5.0) |
| Imports | bluster, edgeR, ggplot2, grDevices, grid, igraph, Matrix, methods, S4Vectors, SingleCellExperiment, splines, stats, SummarizedExperiment, utils |
| System Requirements | |
| URL | https://github.com/Monash-Li-Lab/scProkaR |
| Bug Reports | https://github.com/Monash-Li-Lab/scProkaR/issues |
See More
| Suggests | batchelor, BiocNeighbors, BiocSingular, BiocStyle, cluster, DropletUtils, FNN, harmony, irlba, knitr, RANN, rmarkdown, scrapper (>= 1.0.0), SeuratObject, testthat (>= 3.0.0), uwot |
| Linking To | |
| Enhances | |
| Depends On Me | |
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| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/scProkaR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/scProkaR |
| Package Short Url | https://bioconductor.org/packages/scProkaR/ |
| Package Downloads Report | Download Stats |