This is the released version of cogeqc; for the devel version, see cogeqc.
Systematic quality checks on comparative genomics analysesBioconductor version: Release (3.21)
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: FabrÃcio Almeida-Silva [aut, cre] ORCID: 0000-0002-5314-2964 , Yves Van de Peer [aut] ORCID: 0000-0003-4327-3730
Maintainer: FabrÃcio Almeida-Silva <fabricio_almeidasilva at hotmail.com>
Citation (from within R, entercitation("cogeqc")): Installation
To install this package, start R (version "4.5") 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.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("cogeqc")Follow Installation instructions to use this package in your R session.
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