cogeqc

DOI: 10.18129/B9.bioc.cogeqc    

Systematic quality checks on comparative genomics analyses

Bioconductor version: Release (3.15)

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 quality with BUSCOs; 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 "4.2") 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
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 1.0.0
In Bioconductor since BioC 3.15 (R-4.2) (< 6 months)
License GPL-3
Depends R (>= 4.2.0)
Imports utils, stats, rlang, methods, reshape2, dplyr, ggplot2, ggtree, patchwork, igraph, Biostrings
LinkingTo
Suggests testthat (>= 3.0.0), 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_1.0.0.tar.gz
Windows Binary cogeqc_1.0.0.zip
macOS 10.13 (High Sierra) cogeqc_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/cogeqc
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/cogeqc
Package Short Url https://bioconductor.org/packages/cogeqc/
Package Downloads Report Download Stats

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