Release History
Version 0.3.5
[BAF] add allele flip status for each gene in Local phasing and Global phasing
[minor debug] baf_bias_mode configs update in BAF module
[minor debug] add check cell quality in RDR extra_preprocess.[DEVELOP FOR ST](need test more)
[Analysis] initialize reference cells detection function (from BAF) (todo)
[BAF] update BAF theo ref strategy in wrap BAF module (if refernce cells is limited)
[BAF] test 2 BAF theo ref strategies in wrap BAF module (if refernce cells is limited)
[RDR] update RDR guide ratio correct strategy
[Main update] default params setting for low coverage datasets
[mm10 extension init] update mm10 genes and extend to mm10 application
[Spatial extension init] add some params for spatial transcriptomics
[Spatial filter Genes] set lower min_gene_keep_num in RDR module
[RDR denoise] add function to use BAF information denoisde RDR layer before combination[test now]
[BAF] minor update to get its own KNN connectivities instead of connectivities_expr
[RDR] Reference cell usage strategy update (for multiple celltyps as reference)[init]
[Combine] Special WGD warning function in the combine module.
[Spatial] add spatial coordinates in adata.
[Spatial] debug some preprocessins issues to adapt to spatial cases.
Version 0.3.4
remove deprecated funcs
update plotting tool, mainly in color settings
update xclone tutorials in version 0.3.4
BAF local phasing improvement
BAF module support 3 and 5 allele bias states
Combine module support prob correct mode for copy gain
Combine module support prob correct mode for copy loss (default)
update libratio capping and add cell filter limits
use counts ratio as default
libratio fitting update
provide new denoise function (denoise by cluster)
add ROC evaluation function in analysis module
add functions for XClone clustering
wrap independent plotting modules
potential init to add predefined segmentation
minor debug on BAF guide allele bias ratio
add tutorials in xclone plotting #
add tutorials in xclone data analysis #
Version 0.3.3
Add tutorials for data loadding
Wrap data loading for 3 main modules
try supporting h5py higher version
provide func to get results of different resolution (for benchmarking)
updates in config: add default Smartseq_Config
minor updates in other modules’ configs and general configs
BAF module update: feature specific concentration; extreme DP detection and rescaling(test)
RDR module update: guide chr exclude chr X&Y
more protecting steps in wrapped main module
Version 0.3.2
fix bugs in loadding demo datasets
Version 0.3.1
Wrap 3 main modules: RDR, BAF and Combine
Add tutorials and documentations
Provide demo data
Version 0.3.0
Alpha version of XClone released