Release History

Version 0.4.1

  • [BAF] Improve BAF local phasing

  • [Combine] Add normal and tumor cell classification output

  • [Combine] Add clone level CNA state output

  • [Fix bug] Fix some minor bugs

Version 0.4.0

  • [RDR] Support multiple reference cell types

  • [RDR] Changed RDR to Gaussian Mixture Model (GMM) based

  • [RDR] Add adaptive baseline

  • [RDR] Add new denoising and smoothing methods

  • [BAF] Improve BAF global phasing

  • [Combine] Modified combining strategy

  • [Fix bug] Fix some minor bugs

Version 0.3.9

  • [preprocessing] Add RDR-ONLY read function.

  • [compatibility] Solve the issues caused by scipy expired deprecations in version 1.14.0

  • [Spatial] Aalysis update

  • [Fix bug] RDR BAF data mapping checking in Combine module

  • [improve efficiency] add develop mode (users are recommended to deactive develop mode)

  • [improve efficiency] reduce the memory used in whole pipeline

  • [improve efficiency] only save final results

  • [improve efficiency] improve plotting

  • [docs] add tutorials for annotate reference from BAF module

  • [tutorial] add script demo

  • [tutorial] add RDR-ONLY tutorial

Version 0.3.8

  • [docs] Base Configurations class.

Version 0.3.7

  • [docs] Main functions.

Version 0.3.6

  • [installation] update Dependency for installation

  • [FAQ] Comprehensive tutorials on installation and Dependency

  • [Python version supporting] XClone support Python “==3.7 or >=3.9” adding a nonzero scalar to a sparse array is not supported by scipy in Python > 3.7 (which exists in RDR_smothing functions).

  • [analysis] minor update in Clone function XClustering

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.

  • [preprocessing] change default anno header from “cell” to “barcode”

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