added UMAP clustering
improved domain plot #110
option to change font
option to show gene names
option to sort genes by defined list
option to upload preprocessed data from an input folder
option to specify version for OrthoDB
fixed detailed plot when name of a taxon is substring of another
show supertaxon names when rotate the profile plot
fixed clustering method not applied
check if taxonomy DB exists in cwd instead of r/library
fixed bug wrong order in detailed plot
fixed bug mVar for co-orthologs
extended options in config file
option to specify IP and port
able to generate domain plot from main/customized profile tab
highlight multiple genes/taxa; division lines for taxon group (#110)
simplify gene IDs in detailed plot; show taxonomy hierarchy (#110)
option to filter features in architecture plot (#110)
option to show all input taxa (#110)
added more info to domain plot (e-value, bit-score, pHMM)
option to specify host and port for runPhyloProfile() fn
fixed bug when lowest rank is subspecies
improved highlighted duplicated ortho IDs
fixed bug ordering genes
auto identify lowest rank
option to use user defined taxonomy DB (#124)
option for highlight duplicated ortholog IDs
option for cluster profiles based on ortholog IDs
speedup by pre-calculating taxonomy tree (#123)
disable rank selection after plotting
turn on profile clustering by default
changed "ftp://" to "https://" for taxdmp.zip
fixed #126
option for uploading sorted taxon list
fixed bug ordering gene IDs when using gene categories
fixed bug multiple entries for one (super)taxon ID
fixed bug download data
fixed bug customized profile not showed
added number of co-orthologs and number of taxa in each supertaxon
replaced pfam link by interpro url
fixed bug parsing taxon names for input with more than 9999 taxa
fixed bug button for tree uploading disappear #119
improved parsing seq ID to create links for external DB #117
fixed bug grepping domains for group comparison fn
fixed bug parsing data for a list of input gene IDs #122
option to identify sequence source
added functions for exporting plot settings
fixed error reading taxonNamesReduced.txt that contains "#"
added functions for import and export taxonomy DB
fixed bug of group comparison function
fixed loading cluster from config file
do not show pfam links for smart domains and vice versa
only mainInput is required in config file
use config file for input files, refspec selection and othes settings
turn off auto sizing for large number of taxa or genes (>= 10.000)
fixed filter for "species relation"
added midpoint colors
increase default font size for profile and domain plot
make links to DBs: ncbi taxonomy, ncbi protein, uniprot, pfam, smart
modified taxonomy ranks (ropensci#875)
improved rank indexing function (ropensci#874)
improved x-axis label (#116)
domain plot works with group ID containing pipe
added check for invalid ids in newTaxa file
fixed bug comparing unk taxon IDs with max ncbi taxID
fixed bug comparing taxon IDs with max ncbi taxID
fixed bug filterProfileData (some filtered data could not be plotted)
Add auto sizing feature
Fixed orthoxml parsing function
Plot background for NA orthologs
Fixed highlight by categories
Fixed error when parsing large amount of new taxa
Improved the speed of parsing new taxa
Apply filter to refspec orthologs when not working with strain/species
Fixed bug data lost after filtering var2
Add filter data to detailed plot
Add filter number of co-orthologs to parseInfoProfile()
Calculate percentage of present taxa after filtering of var1 and var2
Fixed filter when working with high taxonomy ranks
Added new NCBI taxonomy ranks (e.g. biotype, isolate, pathogroup, ...)
Added function to reset taxonomy data
Solved problem with new NCBI taxonomy rank "clade" by replace them with "norank"
Fixed bug customized profile of subset of taxa not clickable
Fixed bug checking invalid taxon IDs
Fixed bug in rankIndexing and processNcbiTaxonomy
Improved check for invalid input taxon IDs
Added pseudo IDs for Holozoa and Holomycota clades and their non-NCBI sub-clades
Increased the resolution of the phylostratigraphy function
Improved the rank indexing function
Removed grDevices, grid, stats, utils from Imports list in DESCRIPTION
Added progress indicators for data loading and processing steps
Removed shinycssloaders
Fixed bug listing taxa by selecting a supertaxon from a higher level
Added message for downloading preprocessed data
Fixed bug sorting taxa when taxonomy rank is set as strain
Commented examples of OMA parser functions
Turned off tests for OMA parser functions
Submitted to Bioconductor