Inference And Analysis Of Synteny Networks

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Documentation for package ‘syntenet’ version 1.11.2

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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_bidirectional_hits	Collapse a list of bidirectional DIAMOND hits
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
make_bidirectional	Create a data frame of bidirectional comparisons from unidirectional comparisons
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