v1.5.6

pp Module

• Added mt_startswith argument to control the qc in mouse or other species.

utils Module

• Added schist method to cluster the single cell RNA-seq

single Module

• Fixed the import error of palantir in SEACells
• Added CEFCON model to identify the driver regulators of cell fate decisions

bulk2single Module

• Added use_rep and neighbor_rep argument to configure the nocd

space Module:

• Added SpaceFlow to identify the pseudo-spatial map

v1.5.5

pp Module:

• Added max_cells_ratio and max_genes_ratio to control the max threshold in qc of scRNA-seq

single Module:

• Added SEACells model to calculate the metacells from scRNA-seq

space Module:

• Added STAligner to integrate multi stRNA-seq

v1.5.4

bulk Module:

• Fixed an error in pyDEG.deg_analysis when n_cpus can not be set in pyDeseq2(v0.4.3)

single Module:

• Fixed an argument error in single.batch_correction of combat

utils Module:

• Added venn4 plot to visualize
• Fixed the label visualization of plot_network
• Added ondisk argument of LDA_topic

space Module:

• Added Tangram to mapping the scRNA-seq to stRNA-seq

v1.5.3

single Module:

• Added scVI and MIRA to remove batch effect

space Module:

• Added STAGATE to cluster and denoisy the spatial RNA-seq

pp Module:

• Added doublets argument of ov.pp.qc to control doublets('Default'=True)

v1.5.2

bulk2single Module:

• Resolved a matrix error occurring when gene symbols are not unique.
• Addressed the interpolation issue in BulkTrajBlend when target cells do not exist.
• Corrected the generate function in BulkTrajBlend.
• Rectified the argument for vae_configure in BulkTrajBlend when cell_target_num is set to None.
• Introduced the parameter max_single_cells for input in BulkTrajBlend.
• Defaulted to using scaden for deconvolution in Bulk RNA-seq.

single Module:

• Fixed an error in pyVIA when the root is set to None.
• Added the TrajInfer module for inferring cell trajectories.
• Integrated Palantir and Diffusion_map into the TrajInfer module.
• Corrected the parameter error in batch_correction.

utils Module:

• Introduced plot_pca_variance_ratio for visualizing the ratio of PCA variance.
• Added the cluster and filtered module for clustering the cells
• Integrated MiRA to calculate the LDA topic

v1.5.1

v 1.5.1

single module

• add scLTNN to infer the cell trajectory

bulk2single module

• Update the cell fraction prediction with TAPE in bulk2single
• Fix the group and normalization in bulk2single

utils module

• add Ro/e calculated (by:Haihao Zhang)
• add cal_paga and plot_paga to visualize the state transfer matrix
• fix the read function

v1.4.17

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

v1.4.14

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

v1.4.12

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

v1.4.4

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