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>

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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


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
Suggests testthat (>= 3.0.0), sessioninfo, knitr, BiocStyle, rmarkdown, covr
SystemRequirements BUSCO (>= 5.1.3)
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