scFeatureFilter
This is the released version of scFeatureFilter; for the devel version, see scFeatureFilter.
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]
, Anagha Joshi [aut]
Maintainer: Guillaume Devailly <gdevailly at hotmail.com>
citation("scFeatureFilter")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 | ||
| NEWS | Text | |
| LICENSE | Text |
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 |
See More
| Suggests | testthat, knitr, rmarkdown, BiocStyle, MASS, SingleCellExperiment, SummarizedExperiment, scRNAseq, cowplot |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/scFeatureFilter/ |
| Package Short Url | https://bioconductor.org/packages/scFeatureFilter/ |
| Package Downloads Report | Download Stats |