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fCCAC

functional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing datasets


Bioconductor version: Release (3.18)

Computational evaluation of variability across DNA or RNA sequencing datasets is a crucial step in genomics, as it allows both to evaluate reproducibility of replicates, and to compare different datasets to identify potential correlations. fCCAC applies functional Canonical Correlation Analysis to allow the assessment of: (i) reproducibility of biological or technical replicates, analyzing their shared covariance in higher order components; and (ii) the associations between different datasets. fCCAC represents a more sophisticated approach that complements Pearson correlation of genomic coverage.

Author: Pedro Madrigal [aut, cre]

Maintainer: Pedro Madrigal <pmadrigal at ebi.ac.uk>

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

Installation

To install this package, start R (version "4.3") and enter:


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

BiocManager::install("fCCAC")

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("fCCAC")
fCCAC Vignette PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews ATACSeq, ChIPSeq, Coverage, Epigenetics, FunctionalGenomics, MNaseSeq, RNASeq, Sequencing, Software, Transcription
Version 1.28.0
In Bioconductor since BioC 3.4 (R-3.3) (7.5 years)
License Artistic-2.0
Depends R (>= 4.2.0), S4Vectors, IRanges, GenomicRanges, grid
Imports fda, RColorBrewer, genomation, ggplot2, ComplexHeatmap, grDevices, stats, utils
System Requirements
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Suggests RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown
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Package Archives

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

Source Package fCCAC_1.28.0.tar.gz
Windows Binary fCCAC_1.28.0.zip (64-bit only)
macOS Binary (x86_64) fCCAC_1.28.0.tgz
macOS Binary (arm64) fCCAC_1.28.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/fCCAC
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/fCCAC
Bioc Package Browser https://code.bioconductor.org/browse/fCCAC/
Package Short Url https://bioconductor.org/packages/fCCAC/
Package Downloads Report Download Stats