Files in irycisBioinfo/PATO

Pangenome Analysis Toolkit

BinaryFiles

DESCRIPTION

LICENSE.md

Meta/vignette.rds

NAMESPACE

R/accnet.R R/accnet_enrichment_analysis.R R/accnet_with_padj.R R/annotate.R R/as.data.frame.nr_list.R R/classifier.R R/cluster_accnet.R R/cluster_files_from_distance.R R/cluster_knnn.R R/cluster_mash.R R/clustering.R R/coincidents.R R/core_genome.R R/core_plots.R R/core_snp_genome.R

R/core_snp_genome.R.bak

R/core_snps_matrix.R R/dn_ds.R R/eggnogmapper.R R/export_accnet_aln.R R/export_core_to_fasta.R R/export_to_gephi.R R/extract_non_redundant.R R/heatmap_of_annotation.R R/install_db.R R/knnn.R R/load_gff_list.R R/mash.R R/mmseqs.R R/network_of_annotation.R R/non_redundant.R R/non_redundant_hier.R R/non_redundant_pangenomes.R R/outliers.R R/pagenomes_from_mmseqs.R R/pangenomes_from_files.R R/pangenomes_from_files_mmseqs.R R/pangenomes_mmseq.R R/plasmidome.R R/plot_knnn_network.R R/remove_outliers.R R/screening.R R/sharedness.R R/similarity_network.R R/similarity_tree.R R/singles.R R/snps_map.R R/snps_pairwaise.R R/twins.R R/umap_plot.R README.md

cd

doc/vignette.R doc/vignette.Rmd

doc/vignette.html

inst/bedtools

inst/blast_parser.pl

inst/blast_parser_dnds.pl

inst/cluster_parser.pl

inst/gff_split.pl

inst/k8

inst/mash

inst/mash.macos

inst/minimap2

inst/mmseqs.avx2

inst/mmseqs.macos

inst/mmseqs.sse41

inst/msa2table.pl

inst/paftools.js

man/accnet.Rd man/accnet_enrichment_analysis.Rd man/accnet_with_padj.Rd man/annotate.Rd man/as.data.frame.nr_list.Rd man/classifier.Rd man/cluster_accnet.Rd man/cluster_files_from_distance.Rd man/cluster_knnn.Rd man/cluster_mash.Rd man/clustering.Rd man/coincidents.Rd man/core_genome.Rd man/core_plots.Rd man/core_snp_genome.Rd man/core_snps_matrix.Rd man/dn_ds.Rd man/eggnogmapper.Rd man/export_accnet_aln.Rd man/export_core_to_fasta.Rd man/export_to_gephi.Rd man/extract_non_redundant.Rd man/heatmap_of_annotation.Rd man/install_db.Rd man/knnn.Rd man/load_gff_list.Rd man/mash.Rd man/mmseqs.Rd man/network_of_annotation.Rd man/non_redundant.Rd man/non_redundant_hier.Rd man/non_redundant_pangenomes.Rd man/outliers.Rd man/pangenomes_from_files.Rd man/pangenomes_from_files_mmseqs.Rd man/pangenomes_from_mmseqs.Rd man/pangenomes_mmseqs.Rd man/plasmidome.Rd man/plot_knnn_network.Rd man/remove_outliers.Rd man/screening.Rd man/sharedness.Rd man/similarity_network.Rd man/similarity_tree.Rd man/singles.Rd man/snps_map.Rd man/snps_pairwaise.Rd man/twins.Rd man/umap_plot.Rd

pato.Rproj

vignettes/.gitignore

vignettes/Accnet_800.png

vignettes/Accnet_800_enr.png

vignettes/CoincidentsComp.png

vignettes/CoincidentsHeatmap.png

vignettes/Core_tree.png

vignettes/FunctionsTable.png

vignettes/Heatmap_sharedness.png

vignettes/PATO_bench_pansize.png

vignettes/PATO_benchmarking.png

vignettes/PatoBenchmarking.png

vignettes/SnpMatrixPairwise.png

vignettes/SnpMatrixRoaryLike.png

vignettes/SnpMatrixSnippyLike.png

vignettes/TablaFuncionesPato.pdf

vignettes/TransmissionTreeCore.png

vignettes/TransmissionTreeCoreSNP.png

vignettes/TransmissionTreeMash.png

vignettes/TreeComparison.png

vignettes/acc_ml_tree.png

vignettes/annotation_heatmap.pdf

vignettes/annotation_network.png

vignettes/benchClustering.png

vignettes/cluster-mode-connectedcomp.png

vignettes/cluster-mode-greedyincremental.png

vignettes/cluster-mode-setcover.png

vignettes/clustering_bench_umap.png

vignettes/core_plot.png

vignettes/cov_mode.png

vignettes/diagram.png

vignettes/gephi.png

vignettes/knnn_plot.png

vignettes/knnn_plot_w_cluster.png

vignettes/logo.png

vignettes/outliers.png

vignettes/pangenomes.png

vignettes/snp_heatmap.png

vignettes/tabla.html

vignettes/tanglegram.png

vignettes/tree_mash.png

vignettes/umap_w_colors.png

vignettes/umap_wo_colors.png

vignettes/vignette.R vignettes/vignette.Rmd

irycisBioinfo/PATO documentation built on Oct. 19, 2023, 3:07 p.m.