v1.4.0

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

v1.3.1

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

v.1.2.11

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.

v.1.3.0

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

v.1.2.10

renamed the package to omicverse

single module

• fix the argument error of pySCSA

bulk2single module

• update the plot argument of bulk2single

v1.2.9

bulk module

• fix the duplicates_index mapping of Matrix_ID_mapping
• fix the hub genes plot of pyWGCNA.plot_sub_network
• fix the backupgene of pyGSEA.geneset_enrichment to support the rare species
• add the module matrix plot in pyWGCNA.plot_matrix

single module

• add the rank_genes_groups check in pySCSA

bulk2single module

• fix the import error of deepforest

v.1.2.8

Install

• fix the error of pip in install

bulk2single module

• Change the deep-forest of Single2Spatial to Neuron Network to perform classification task
• The entire Single2Spatial inference process is accelerated using the GPU, and can be estimated at the batch level by modifying the set predicted_size, the original author's function is estimated spot by spot, which is very inefficient
• Update the logical of Single2Spatial.load to accelerate model loading

v.1.2.5

single module:

• Add pyVIA module include run, plot_piechart_graph, plot_stream, plot_trajectory_gams, plot_lineage_probability, plot_gene_trend, plot_gene_trend_heatmap, plot_clustergraph
• Fix the error of warning of utils.pyomic_plot_set
• Update the requirements included pybind11, hnswlib, termcolor, pygam, pillow, gdown

v.1.2.1

single module:

• Add pySCSA module included cell_anno, cell_anno_print, cell_auto_anno, get_model_tissue
• Update the pySCSA tutorial that can be found at here
• Add filter the doublets cells of single.scanpy_lazy
• Add single.scanpy_cellanno_from_dict to annotate easier
• Updated the database of SCSA from CellMarker2.0
• Fix the error database key Ensembl_HGNC and Ensembl_Mouse of SCSA

v1.2.0

Update bulk and bulk2single code reference

bulk module:

• Fix the cutoff parameter non-vaild on bulk.geneset_enrichment
• Add pyPPI,pyGSEA,pyWGCNA,pyTCGA,pyDEG module.

bulk2single module:

• Add the bulk2single.save to save model by manual