Package: cogeqc 1.11.0
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:
cogeqc_1.11.0.tar.gz
cogeqc_1.11.0.zip(r-4.5)cogeqc_1.11.0.zip(r-4.4)cogeqc_1.11.0.zip(r-4.3)
cogeqc_1.11.0.tgz(r-4.4-any)cogeqc_1.11.0.tgz(r-4.3-any)
cogeqc_1.11.0.tar.gz(r-4.5-noble)cogeqc_1.11.0.tar.gz(r-4.4-noble)
cogeqc_1.11.0.tgz(r-4.4-emscripten)cogeqc_1.11.0.tgz(r-4.3-emscripten)
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')) |
Bug tracker:https://github.com/almeidasilvaf/cogeqc/issues
- 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-1.11.0(bioc 3.21)cogeqc-1.10.0(bioc 3.20)
softwaregenomeassemblycomparativegenomicsfunctionalgenomicsphylogeneticsqualitycontrolnetworkcomparative-genomicsevolutionary-genomics
Last updated 2 months agofrom:8c60dba3bb. Checks:OK: 6 ERROR: 1. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 19 2024 |
| R-4.5-win | OK | Dec 19 2024 |
| R-4.5-linux | ERROR | Dec 19 2024 |
| R-4.4-win | OK | Dec 19 2024 |
| R-4.4-mac | OK | Dec 19 2024 |
| R-4.3-win | OK | Dec 19 2024 |
| R-4.3-mac | OK | Dec 19 2024 |
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:apeaplotaskpassbeeswarmBiocGenericsBiostringsclicolorspacecpp11crayoncurldigestdplyrfansifarverfsgenericsGenomeInfoDbGenomeInfoDbDataggbeeswarmggfunggplot2ggplotifyggtreegluegridGraphicsgtablehttrigraphIRangesisobandjsonlitelabelinglatticelazyevallifecyclemagrittrMASSMatrixmgcvmimemunsellnlmeopensslpatchworkpillarpkgconfigplyrpurrrR6RColorBrewerRcppreshape2rlangS4VectorsscalesstringistringrsystibbletidyrtidyselecttidytreetreeioUCSC.utilsutf8vctrsviporviridisLitewithrXVectoryulab.utilszlibbioc
Assessing genome assembly and annotation quality
Rendered fromvignette_01_assessing_genome_assembly.Rmdusingknitr::rmarkdownon Dec 19 2024.Last update: 2023-01-23
Started: 2022-01-06
Assessing orthogroup inference
Rendered fromvignette_02_assessing_orthogroup_inference.Rmdusingknitr::rmarkdownon Dec 19 2024.Last update: 2023-10-07
Started: 2022-01-07
Assessing synteny identification
Rendered fromvignette_03_assessing_synteny.Rmdusingknitr::rmarkdownon Dec 19 2024.Last update: 2022-10-20
Started: 2022-01-30
