scFeatureFilter

This is the released version of scFeatureFilter; for the devel version, see scFeatureFilter.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7

A correlation-based method for quality filtering of single-cell RNAseq data

Bioconductor version: Release (3.23)

An R implementation of the correlation-based method developed in the Joshi laboratory to analyse and filter processed single-cell RNAseq data. It returns a filtered version of the data containing only genes expression values unaffected by systematic noise.

Author: Angeles Arzalluz-Luque [aut], Guillaume Devailly [aut, cre] ORCID: 0000-0001-8878-9357 , Anagha Joshi [aut]

Maintainer: Guillaume Devailly <gdevailly at hotmail.com>

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

Angeles Arzalluz-Luque, Guillaume Devailly, Anagha Joshi. scFeatureFilter: A correlation-based method for quality filtering of single-cell RNAseq data. doi:10.18129/B9.bioc.scFeatureFilter, R package version 1.32.0, https://bioconductor.org/packages/scFeatureFilter.

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")

BiocManager::install("scFeatureFilter")

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("scFeatureFilter")

Introduction to scFeatureFilter	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GeneExpression, ImmunoOncology, Preprocessing, RNASeq, SingleCell, Software
Version	1.32.0
In Bioconductor since	BioC 3.7 (R-3.5) (8.5 years)
License	MIT + file LICENSE
Depends	R (>= 4.5.0)
Imports	dplyr (>= 0.7.3), ggplot2 (>= 2.1.0), magrittr (>= 1.5), rlang (>= 0.1.2), tibble (>= 1.3.4), stats, methods
System Requirements
URL	https://bioconductor.org/packages/scFeatureFilter/
Bug Reports	https://github.com/gdevailly/scFeatureFilter/issues

Suggests	testthat, knitr, rmarkdown, BiocStyle, MASS, SingleCellExperiment, SummarizedExperiment, scRNAseq, cowplot
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	scFeatureFilter_1.32.0.tar.gz
Windows Binary (x86_64)	scFeatureFilter_1.32.0.zip
macOS Binary (big-sur-x86_64)	scFeatureFilter_1.32.0.tgz
macOS Binary (sonoma-arm64)	scFeatureFilter_1.32.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/scFeatureFilter
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/scFeatureFilter
Package Short Url	https://bioconductor.org/packages/scFeatureFilter/
Package Downloads Report	Download Stats