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Commits : Listings

Analyzed about 9 hours ago. based on code collected about 9 hours ago.
Jul 18, 2024 — Jul 18, 2025
Commit Message Contributor Files Modified Lines Added Lines Removed Code Location Date
improve algorithms.synteny.summary()
tanghaibao
as Haibao Tang
More... about 13 years ago
allow shades that cross the same track (duplication shades) in graphics.karyotype
tanghaibao
as Haibao Tang
More... about 13 years ago
move read_trees() function to graphics.tree
tanghaibao
as Haibao Tang
More... about 13 years ago
fix target bug in utils.cbook.human_size
tanghaibao
as Haibao Tang
More... about 13 years ago
wrap the heavy drawing in class so that they can be called separated to form composite figures; affects graphics.karyotype and graphics.synteny
tanghaibao
as Haibao Tang
More... about 13 years ago
Use a different font in graphics.base
tanghaibao
as Haibao Tang
More... about 13 years ago
add highlight blocks functionality in graphics.karyotype
tanghaibao
as Haibao Tang
More... about 13 years ago
minor changes in graphics.synteny
tanghaibao
as Haibao Tang
More... about 13 years ago
add algorithms.synteny.matrix() to write Oxford grid
tanghaibao
as Haibao Tang
More... about 13 years ago
add option --auto to graphics.karyotype
tanghaibao
as Haibao Tang
More... about 13 years ago
added synteny layout heuristic in graphics.karyotype
tanghaibao
as Haibao Tang
More... about 13 years ago
add ShadeManager to graphics.karyotype
tanghaibao
as Haibao Tang
More... about 13 years ago
modify graphics.chromosome.HorizontalChromosome
tanghaibao
as Haibao Tang
More... about 13 years ago
add graphics.karyotype to plot macrosynteny
tanghaibao
as Haibao Tang
More... about 13 years ago
add algorithms.synteny.screen() to extract certain blocks
tanghaibao
as Haibao Tang
More... about 13 years ago
add algorithms.quota (QUOTA-ALIGN, Tang et al. BMC Bioinformatics 2011)
tanghaibao
as Haibao Tang
More... about 13 years ago
add more reporting to algorithms.synteny.mcscan() and output screened block ids
tanghaibao
as Haibao Tang
More... about 13 years ago
do not strip names when importing filtered BLAST
tanghaibao
as Haibao Tang
More... about 13 years ago
add option --tree in graphics.synteny
tanghaibao
as Haibao Tang
More... about 13 years ago
add option MIN_CONTIG=300 to Allpaths script
tanghaibao
as Haibao Tang
More... about 13 years ago
highlight shades if line startswith asterisk in graphics.synteny
tanghaibao
as Haibao Tang
More... about 13 years ago
shade implemented in graphics.synteny
tanghaibao
as Haibao Tang
More... about 13 years ago
make tracks and glyphs rotate in graphics.synteny
tanghaibao
as Haibao Tang
More... about 13 years ago
read in configuration file to plot local synteny in graphics.synteny()
tanghaibao
as Haibao Tang
More... about 13 years ago
add graphics.paper as a repo for figures in past manuscripts
tanghaibao
as Haibao Tang
More... about 13 years ago
fix reporting of depths when self-self comparison
tanghaibao
as Haibao Tang
More... about 13 years ago
when mcscan() works on self-self comparison, report both blocks
tanghaibao
as Haibao Tang
More... about 13 years ago
add option --coverage to assembly.kmer.histogram()
tanghaibao
as Haibao Tang
More... about 13 years ago
add option --Nm to algorithms.synteny.mcscan()
tanghaibao
as Haibao Tang
More... about 13 years ago
prevent liftover pairs outside the bounds of the original core synteny blocks
tanghaibao
as Haibao Tang
More... about 13 years ago