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 (3.24)
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("cogeqc")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text |
Details
| biocViews | ComparativeGenomics, FunctionalGenomics, GenomeAssembly, Network, Phylogenetics, QualityControl, Software |
| Version | 1.17.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (4.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.2.0) |
| Imports | utils, graphics, stats, methods, reshape2, ggplot2, scales, ggtree, patchwork, igraph, rlang, ggbeeswarm, jsonlite, Biostrings |
| 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_1.17.0.tar.gz |
| Windows Binary (x86_64) | cogeqc_1.17.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | cogeqc_1.17.0.tgz |
| macOS Binary (sonoma-arm64) | cogeqc_1.17.0.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 |