chevreulProcess

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see chevreulProcess.

Tools for managing SingleCellExperiment objects as projects

Bioconductor version: 3.21

Tools analyzing SingleCellExperiment objects as projects. for input into the Chevreul app downstream. Includes functions for analysis of single cell RNA sequencing data. Supported by NIH grants R01CA137124 and R01EY026661 to David Cobrinik.

Author: Kevin Stachelek [aut, cre] ORCID iD ORCID: 0000-0003-2085-695X , Bhavana Bhat [aut]

Maintainer: Kevin Stachelek <kevin.stachelek at gmail.com>

Citation (from within R, enter citation("chevreulProcess")):

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("chevreulProcess")

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("chevreulProcess")

Preprocessing HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Coverage, DataImport, DimensionReduction, GeneExpression, Normalization, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Transcription, Transcriptomics, Visualization

Version 1.0.0

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

License MIT + file LICENSE

Depends R (>= 4.5.0), SingleCellExperiment, scater

Imports batchelor, bluster, circlize, cluster, DBI, dplyr, EnsDb.Hsapiens.v86, ensembldb, fs, GenomicFeatures, glue, megadepth, methods, purrr, RSQLite, S4Vectors, scran, scuttle, stringr, tibble, tidyr, tidyselect, utils

System Requirements

URL https://github.com/whtns/chevreulProcess https://whtns.github.io/chevreulProcess/

Bug Reports https://github.com/cobriniklab/chevreulProcess/issues

Suggests BiocStyle, knitr, RefManageR, rmarkdown, testthat (>= 3.0.0)

Linking To

Enhances

Depends On Me chevreulPlot, chevreulShiny

Imports Me

Suggests Me

Links To Me

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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package chevreulProcess_1.0.0.tar.gz

Windows Binary (x86_64) chevreulProcess_1.0.0.zip

macOS Binary (x86_64) chevreulProcess_1.0.0.tgz

macOS Binary (arm64) chevreulProcess_1.0.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/chevreulProcess

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/chevreulProcess

Bioc Package Browser https://code.bioconductor.org/browse/chevreulProcess/

Package Short Url https://bioconductor.org/packages/chevreulProcess/

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