cogeqc

DOI: 10.18129/B9.bioc.cogeqc  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see cogeqc.

Systematic quality checks on comparative genomics analyses

Bioconductor version: 3.17

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>

Installation

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

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

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")

 

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

Details

biocViews	ComparativeGenomics, FunctionalGenomics, GenomeAssembly, Network, Phylogenetics, QualityControl, Software
Version	1.4.1
In Bioconductor since	BioC 3.15 (R-4.2) (1.5 years)
License	GPL-3
Depends	R (>= 4.2.0)
Imports	utils, graphics, stats, methods, reshape2, ggplot2, scales, ggtree, patchwork, igraph, rlang, ggbeeswarm, jsonlite, Biostrings
LinkingTo
Suggests	testthat (>= 3.0.0), sessioninfo, knitr, BiocStyle, rmarkdown, covr
SystemRequirements	BUSCO (>= 5.1.3)
Enhances
URL	https://github.com/almeidasilvaf/cogeqc
BugReports	https://support.bioconductor.org/t/cogeqc
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	cogeqc_1.4.1.tar.gz
Windows Binary	cogeqc_1.4.1.zip
macOS Binary (x86_64)	cogeqc_1.4.1.tgz
macOS Binary (arm64)	cogeqc_1.4.1.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