bulk module

• fix the compatibility of pydeseq2 while its version equal 0.4.0
• add bulk.batch_correction for multi bulk RNA-seq/microarray sample

single module

• add single.batch_correction for multi single cell datasets

preprocess module

• add parameter layers_add in pp.scale

bulk module

• add mad_filtered to filtered the robust genes when calculated the network in ov.bulk.pyWGCNA module
• fix string_interaction in ov.bulk.pyPPI for string-db updated.

preprocess module

• change mode arguement of pp.preprocess, normalize|HVGs：We use | to control the preprocessing step, | before for the normalisation step, either shiftlog or pearson, and | after for the highly variable gene calculation step, either pearson or seurat. Our default is shiftlog|pearson.
• add ov.utils.embedding,ov.utils.neighbors, and ov.utils.stacking_vol
• add batch_key in pp.preprocess and pp.qc

utils module

• add plot_ConvexHull to visualize the boundary of clusters
• add weighted_knn_trainer and weighted_knn_transfer for multi adata integrate

single module

• fix the error of import of mofax

v 1.4.12

update conda install omicverse -c conda-forge
add pytest

single module

• add pyTOSICA module in single to perform celltype migration from reference scRNA-seq in Tranformer model
• add atac_concat_get_index,atac_concat_inner,atac_concat_outer function to merge/concat the scATAC data.
• fix MetaTime.predicted when Unknown cell type appear

preprocess module

• add plot_embedding in ov.utils to plot umap in special color dict

single module

• add panglaodb database to pySCSA module
• fix the error of pySCSA.cell_auto_anno when some celltype not found in clusters
• fix the error of pySCSA.cell_anno when rank_genes_groups not consisted with clusters
• add pySIMBA module in single to perform batch correction

preprocess module

• add store_layers and retrieve_layers in ov.utils
• add plot_embedding_celltype and plot_cellproportion in ov.utils

preprocess module

• add pp(preprocess) module included qc(quantity control), hvg(high variable feature), pca
• add data_files for cell cycle calculate from Cellula and pegasus

bulk2single module

• add BulkTrajBlend method in bulk2single

single module

• fix the error of scnocd model
• add save, load, and get_pair_dict of scnocd model

utils

• add mde method in utils
• add gz format support for utils.read

single module

• add get_celltype_marker method in single
• add GLUE_pair, pyMOFA, pyMOFAART module in single
• add tutorial Multi omics analysis by MOFA and GLUE
• update tutorial Multi omics analysis by MOFA

bulk module

• fix wilcoxon method in pyDEG.deg_analysis
• add the parameter setting of treatment and control group's name in pyDEG.plot_boxplot
• fix the figure display not entire of pyWGCNA.plot_matrix
• fix the category correlation failed by ont-hot in pyWGCNA.analysis_meta_correlation
• fix the network display failed in pyWGCNA.plot_sub_network and updated the utils.plot_network to avoid this error.

bulk module

• add DEseq2 method to pyDEG.deg_analysis
• add pyGSEA module in bulk
• change the name of raw pyGSEA to pyGSE in bulk
• add get_gene_annotation of utils to perform gene_name transformation

renamed the package to omicverse

single module

• fix the argument error of pySCSA

bulk2single module

• update the plot argument of bulk2single