Inference And Analysis Of Synteny Networks


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Documentation for package ‘syntenet’ version 1.7.1

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angiosperm_phylogeny Microsynteny-based angiosperm phylogeny.
annotation Filtered genome annotation for Ostreococcus sp. species
binarize_and_transpose Binarize and transpose the phylogenomic profile matrix
blast_list List of data frames containing BLAST-like tabular output
check_input Check if input objects are ready for further analyses
clusters Synteny network clusters of BUSCO genes for 25 eudicot species
cluster_network Cluster the synteny network using the Infomap algorithm
collapse_protein_ids Collapse protein IDs into gene IDs in sequence names of AAStringSet objects
create_species_id_table Create a data frame of species IDs (3-5-character abbreviations)
diamond_is_installed Check if DIAMOND is installed
edges Synteny network of Ostreococcus genomes represented as an edge list
export_sequences Export processed sequences as FASTA files
fasta2AAStringSetlist Read FASTA files in a directory as a list of AAStringSet objects
find_GS_clusters Find group-specific clusters based on user-defined species classification
gff2GRangesList Read GFF/GTF files in a directory as a GRangesList object
infer_microsynteny_phylogeny Infer microsynteny-based phylogeny with IQTREE
infer_syntenet Infer synteny network
interspecies_synteny Detect interspecies synteny
intraspecies_synteny Detect intraspecies synteny
iqtree_is_installed Check if IQTREE is installed
iqtree_version Get IQ-TREE version
last_is_installed Check if last is installed
network Synteny network of BUSCO genes for 25 eudicot species
parse_collinearity Parse .collinearity files obtained with MCScan
phylogenomic_profile Perform phylogenomic profiling for synteny network clusters
plot_network Plot network
plot_profiles Plot a heatmap of phylogenomic profiles
process_input Process sequence data
profiles2phylip Save the transposed binary profiles matrix to a file in PHYLIP format
proteomes Filtered proteomes of Ostreococcus sp. species
rcpp_mcscanx_file rcpp_mcscanx_file
read_diamond Read DIAMOND/BLAST tables as a list of data frames
run_diamond Wrapper to run DIAMOND from an R session
run_last Wrapper to run last from an R session
scerevisiae_annot Genome annotation of the yeast species S. cerevisiae
scerevisiae_diamond Intraspecies DIAMOND output for S. cerevisiae