Package: cogeqc 1.9.0

Fabrício Almeida-Silva

cogeqc: Systematic quality checks on comparative genomics analyses

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.

Authors:Fabrício Almeida-Silva [aut, cre], Yves Van de Peer [aut]

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cogeqc.pdf |cogeqc.html✨
cogeqc/json (API)
NEWS

# Install 'cogeqc' in R:
install.packages('cogeqc', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/almeidasilvaf/cogeqc/issues

Datasets:
  • batch_summary - BUSCO summary output for batch mode
  • interpro_ath - Intepro annotation for Arabidopsis thaliana's genes
  • interpro_bol - Intepro annotation for Brassica oleraceae's genes
  • og - Orthogroups between Arabidopsis thaliana and Brassica oleraceae
  • synnet - Synteny network for Brassica oleraceae, B. napus, and B. rapa
  • tree - Species tree for model species

On BioConductor:cogeqc-1.9.0(bioc 3.20)cogeqc-1.8.0(bioc 3.19)

bioconductor-package

23 exports 0.71 score 76 dependencies

Last updated 2 months agofrom:88dde65859

Exports:assess_orthogroupsassess_synnetassess_synnet_listbusco_is_installedcalculate_Hcompare_genome_statscompare_orthogroupsfit_sftget_genome_statslist_busco_datasetsplot_buscoplot_duplicationsplot_genes_in_ogsplot_genome_statsplot_og_overlapplot_og_sizesplot_orthofinder_statsplot_species_specific_ogsplot_species_treeread_buscoread_orthofinder_statsread_orthogroupsrun_busco

Dependencies:apeaplotaskpassbeeswarmBiocGenericsBiostringscachemclicolorspacecpp11crayoncurldigestdplyrfansifarverfastmapfsgenericsGenomeInfoDbGenomeInfoDbDataggbeeswarmggfunggplot2ggplotifyggtreegluegridGraphicsgtablehttrigraphIRangesisobandjsonlitelabelinglatticelazyevallifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslpatchworkpillarpkgconfigplyrpurrrR6RColorBrewerRcppreshape2rlangS4VectorsscalesstringistringrsystibbletidyrtidyselecttidytreetreeioUCSC.utilsutf8vctrsviporviridisLitewithrXVectoryulab.utilszlibbioc

Assessing genome assembly and annotation quality

Fabricio Almeida-Silva, Yves Van de Peer

Rendered fromvignette_01_assessing_genome_assembly.Rmdusingknitr::rmarkdownon Jul 02 2024.

Last update: 2023-01-23
Started: 2022-01-06

Assessing orthogroup inference

Fabricio Almeida-Silva, Yves Van de Peer

Rendered fromvignette_02_assessing_orthogroup_inference.Rmdusingknitr::rmarkdownon Jul 02 2024.

Last update: 2023-10-07
Started: 2022-01-07

Assessing synteny identification

Fabricio Almeida-Silva, Yves Van de Peer

Rendered fromvignette_03_assessing_synteny.Rmdusingknitr::rmarkdownon Jul 02 2024.

Last update: 2022-10-20
Started: 2022-01-30

Readme and manuals

Help Manual

Help pageTopics
Assess orthogroup inference based on functional annotationassess_orthogroups
Assess synteny network based on graph propertiesassess_synnet
Assess list of synteny networks as in 'assess_synnet'assess_synnet_list
BUSCO summary output for batch modebatch_summary
Check if BUSCO is installedbusco_is_installed
Calculate homogeneity scores for orthogroupscalculate_H
Compare user-defined assembly statistics with statistics of NCBI genomescompare_genome_stats
Compare inferred orthogroups to a reference setcompare_orthogroups
Goodness of fit test for the scale-free topology modelfit_sft
Get summary statistics for genomes on NCBI using the NCBI Datasets APIget_genome_stats
Intepro annotation for Arabidopsis thaliana's genesinterpro_ath
Intepro annotation for Brassica oleraceae's genesinterpro_bol
List BUSCO data setslist_busco_datasets
Orthogroups between Arabidopsis thaliana and Brassica oleraceaeog
Plot BUSCO summary outputplot_busco
Plot species-specific duplicationsplot_duplications
Plot percentage of genes in orthogroups for each speciesplot_genes_in_ogs
Plot statistics on genome assemblies on the NCBIplot_genome_stats
Plot pairwise orthogroup overlap between speciesplot_og_overlap
Plot orthogroup sizes per speciesplot_og_sizes
Plot a panel with a summary of Orthofinder statsplot_orthofinder_stats
Plot number of species-specific orthogroupsplot_species_specific_ogs
Plot species treeplot_species_tree
Read and parse BUSCO's summary reportread_busco
Read and parse Orthofinder summary statisticsread_orthofinder_stats
Read and parse orthogroups file created by OrthoFinderread_orthogroups
Run BUSCO assessment of assembly and annotation qualityrun_busco
Synteny network for Brassica oleraceae, B. napus, and B. rapasynnet
Species tree for model speciestree