Welcome to the new bioconductor.org!

cogeqc

This is the development version of cogeqc; for the stable release version, see cogeqc.

Systematic quality checks on comparative genomics analyses


Bioconductor version: Development (3.19)

cogeqc aims to facilitate systematic quality checks on standard comparative genomics analyses to help researchers detect issues and select the most suitable parameters for each data set. cogeqc can be used to asses: i. genome assembly and annotation quality with BUSCOs and comparisons of statistics with publicly available genomes on the NCBI; ii. orthogroup inference using a protein domain-based approach and; iii. synteny detection using synteny network properties. There are also data visualization functions to explore QC summary statistics.

Author: Fabrício Almeida-Silva [aut, cre] , Yves Van de Peer [aut]

Maintainer: Fabrício Almeida-Silva <fabricio_almeidasilva at hotmail.com>

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("cogeqc")

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("cogeqc")
Assessing genome assembly and annotation quality HTML R Script
Assessing orthogroup inference HTML R Script
Assessing synteny identification HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews ComparativeGenomics, FunctionalGenomics, GenomeAssembly, Network, Phylogenetics, QualityControl, Software
Version 1.7.2
In Bioconductor since BioC 3.15 (R-4.2) (2 years)
License GPL-3
Depends R (>= 4.2.0)
Imports utils, graphics, stats, methods, reshape2, ggplot2, scales, ggtree, patchwork, igraph, rlang, ggbeeswarm, jsonlite, Biostrings
System Requirements BUSCO (>= 5.1.3)
URL https://github.com/almeidasilvaf/cogeqc
Bug Reports https://support.bioconductor.org/t/cogeqc
See More
Suggests testthat (>= 3.0.0), sessioninfo, knitr, BiocStyle, rmarkdown, covr
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 cogeqc_1.7.2.tar.gz
Windows Binary cogeqc_1.7.2.zip
macOS Binary (x86_64) cogeqc_1.7.2.tgz
macOS Binary (arm64) cogeqc_1.7.2.tgz
Source Repository git clone https://git.bioconductor.org/packages/cogeqc
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/cogeqc
Bioc Package Browser https://code.bioconductor.org/browse/cogeqc/
Package Short Url https://bioconductor.org/packages/cogeqc/
Package Downloads Report Download Stats