Release Notes¶

v 1.0.0¶

• First public release.

v 1.1.7¶

bulk module:¶

• Added Deseq2, including pyDEseq functions: deseq2_normalize, estimateSizeFactors, estimateDispersions, Matrix_ID_mapping.
• Included TCGA with TCGA.
• Introduced Enrichment with functions geneset_enrichment, geneset_plot.

single module:¶

• Integrated scdrug with functions autoResolution, writeGEP, Drug_Response.
• Added cpdb with functions cpdb_network_cal, cpdb_plot_network, cpdb_plot_interaction, cpdb_interaction_filtered.
• Included scgsea with functions geneset_aucell, pathway_aucell, pathway_aucell_enrichment, pathway_enrichment, pathway_enrichment_plot.

v 1.1.8¶

single module:¶

• Addressed errors in cpdb, including import errors and color issues in cpdb_plot_network.
• Introduced cpdb_submeans_exacted in cpdb for easy sub-network extraction.

v 1.1.9¶

bulk2single module:¶

• Added the bulk2single module.
• Fixed model load error from bulk2space.
• Resolved early stop issues from bulk2space.
• Included more user-friendly input methods and visualizations.
• Added loss history visualization.

utils module:¶

• Introduced pyomic_palette in the plot module.

v 1.1.10¶

• Updated all code references.

single module:¶

• Fixed non-valid parameters in single.mofa.mofa_run function.
• Added layer raw count addition in single.scanpy_lazy function.
• Introduced utils.plot_boxplot for plotting box plots with jittered points.
• Added bulk.pyDEseq.plot_boxplot for plotting box plots with jittered points for specific genes.

v 1.2.0¶

bulk module:¶

• Fixed non-valid cutoff parameter in bulk.geneset_enrichment.
• Added modules: pyPPI, pyGSEA, pyWGCNA, pyTCGA, pyDEG.

bulk2single module:¶

• Introduced bulk2single.save for manual model saving.

v 1.2.1-4¶

single module:¶

• Added pySCSA module with functions: cell_anno, cell_anno_print, cell_auto_anno, get_model_tissue.
• Implemented doublet cell filtering in single.scanpy_lazy.
• Added single.scanpy_cellanno_from_dict for easier annotation.
• Updated SCSA database from CellMarker2.0.
• Fixed errors in SCSA database keys: Ensembl_HGNC and Ensembl_Mouse.

v 1.2.5¶

single module:¶

• Added pyVIA module with functions: run, plot_piechart_graph, plot_stream, plot_trajectory_gams, plot_lineage_probability, plot_gene_trend, plot_gene_trend_heatmap, plot_clustergraph.
• Fixed warning error in utils.pyomic_plot_set.
• Updated requirements, including pybind11, hnswlib, termcolor, pygam, pillow, gdown.

v 1.2.6¶

single module:¶

• Added pyVIA.get_piechart_dict and pyVIA.get_pseudotime.

v 1.2.7¶

bulk2single module:¶

• Added Single2Spatial module with functions: load, save, train, spot_assess.
• Fixed installation errors for packages in pip.

v 1.2.8¶

• Fixed pip installation errors.

bulk2single module:¶

• Replaced deep-forest in Single2Spatial with Neuron Network for classification tasks.
• Accelerated the entire Single2Spatial inference process using GPU and batch-level estimation by modifying the predicted_size setting.

v 1.2.9¶

bulk module:¶

• Fixed duplicates_index mapping in Matrix_ID_mapping.
• Resolved hub genes plot issues in pyWGCNA.plot_sub_network.
• Fixed backupgene in pyGSEA.geneset_enrichment to support rare species.
• Added matrix plot module in pyWGCNA.plot_matrix.

single module:¶

• Added rank_genes_groups check in pySCSA.

bulk2single module:¶

• Fixed import error of deepforest.

v 1.2.10¶

• Renamed the package to omicverse.

single module:¶

• Fixed argument error in pySCSA.

bulk2single module:¶

• Updated plot arguments in bulk2single.

v 1.2.11¶

bulk module:¶

• Fixed wilcoxon method in pyDEG.deg_analysis.
• Added parameter setting for treatment and control group names in pyDEG.plot_boxplot.
• Fixed figure display issues in pyWGCNA.plot_matrix.
• Fixed category correlation failed by one-hot in pyWGCNA.analysis_meta_correlation.
• Fixed network display issues in pyWGCNA.plot_sub_network and updated utils.plot_network to avoid errors.

v 1.3.0¶

bulk module:¶

• Added DEseq2 method to pyDEG.deg_analysis.
• Introduced pyGSEA module in bulk.
• Renamed raw pyGSEA to pyGSE in bulk.
• Added get_gene_annotation in utils for gene name transformation.

v 1.3.1¶

single module:¶

• Added get_celltype_marker method.

single module:¶

• Added GLUE_pair, pyMOFA, pyMOFAART module.
• Added tutorials for Multi omics analysis by MOFA and GLUE.
• Updated tutorial for Multi omics analysis by MOFA.

v 1.4.0¶

bulk2single module:¶

• Added BulkTrajBlend method.

single module:¶

• Fixed errors in scnocd model.
• Added save, load, and get_pair_dict in scnocd model.

utils module:¶

• Added mde method.
• Added gz format support for utils.read.

v 1.4.1¶

preprocess module:¶

• Added pp (preprocess) module with qc (quantity control), hvg (high variable feature), pca.
• Added data_files for cell cycle calculation from Cellula and pegasus.

v 1.4.3¶

¶

preprocess module: - Fixed sparse preprocess error in pp. - Fixed trajectory import error in via. - Added gene correlation analysis of trajectory.

v 1.4.4¶

single module:¶

• Added panglaodb database to pySCSA module.
• Fixed errors in pySCSA.cell_auto_anno when some cell types are not found in clusters.
• Fixed errors in pySCSA.cell_anno when rank_genes_groups are not consistent with clusters.
• Added pySIMBA module in single for batch correction.

preprocess module:¶

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

v 1.4.5¶

single module:¶

• Added MetaTiME module to perform cell type annotation automatically in TME.

v 1.4.12¶

• Updated conda install omicverse -c conda-forge.

single module:¶

• Added pyTOSICA module to perform cell type migration from reference scRNA-seq in Transformer model.
• Added atac_concat_get_index, atac_concat_inner, atac_concat_outer functions to merge/concatenate scATAC data.
• Fixed MetaTime.predicted when Unknown cell type appears.

preprocess module:¶

• Added plot_embedding in ov.utils to plot UMAP in a special color dictionary.

v 1.4.13¶

bulk module:¶

• Added mad_filtered to filter robust genes when calculating the network in ov.bulk.pyWGCNA module.
• Fixed string_interaction in ov.bulk.pyPPI for string-db updates.

preprocess module:¶

• Changed mode argument of pp.preprocess to control preprocessing steps.
• Added ov.utils.embedding, ov.utils.neighbors, and ov.utils.stacking_vol.

v 1.4.14¶

preprocess module:¶

• Added batch_key in pp.preprocess and pp.qc.

utils module:¶

• Added plot_ConvexHull to visualize the boundary of clusters.
• Added weighted_knn_trainer and weighted_knn_transfer for multi-adata integration.

single module:¶

• Fixed import errors in mofa.

v 1.4.17¶

bulk module:¶

• Fixed compatibility issues with pydeseq2 version 0.4.0.
• Added bulk.batch_correction for multi-bulk RNA-seq/microarray samples.

single module:¶

• Added single.batch_correction for multi-single cell datasets.

preprocess module:¶

• Added parameter layers_add in pp.scale.

v 1.5.0¶

single module:¶

• Added cellfategenie to calculate timing-associated genes/genesets.
• Fixed the name error in atac_concat_outer.
• Added more kwargs for batch_correction.

utils module:¶

• Added plot_heatmap to visualize the heatmap of pseudotime.
• Fixed embedding when the version of mpl is larger than 3.7.0.
• Added geneset_wordcloud to visualize geneset heatmaps of pseudotime.

v 1.5.1¶

single module:¶

• Added scLTNN to infer cell trajectory.

bulk2single module:¶

• Updated cell fraction prediction with TAPE in bulk2single.
• Fixed group and normalization issues in bulk2single.

utils module:¶

• Added Ro/e calculation (by: Haihao Zhang).
• Added cal_paga and plot_paga to visualize the state transfer matrix.
• Fixed the read function.

v 1.5.2¶

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

v 1.5.3¶

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)

v 1.5.4¶

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

v 1.5.5¶

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

v 1.5.6¶

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

v 1.5.8¶

pp Module¶

• Added score_genes_cell_cycle function to calculate the cell cycle

bulk Module¶

• Fixed dds.plot_volcano text plot error when the version of adjustText larger than 0.9

single Module¶

• Optimised MetaCell.load model loading logic
• Fixed an error when loading the model usng MetaCell.load
• Added tutorials of Metacells

pl Module¶

Add pl as a unified drawing prefix for the next release, to replace the drawing functionality in the original utils, while retaining the drawing in the original utils.

• Added embedding to plot the embedding of scRNA-seq using ov.pl.embedding
• Added optim_palette to provide a spatially constrained approach that generates discriminate color assignments for visualizing single-cell spatial data in various scenarios
• Added cellproportion to plot the proportion of stack bar of scRNA-seq
• Added embedding_celltype to plot the figures both celltype proportion and embedding
• Added ConvexHull to plot the ConvexHull around the target cells
• Added embedding_adjust to adjust the text of celltype legend in embedding
• Added embedding_density to plot the category density in the cells
• Added bardotplot to plot the bardotplot between different groups.
• Added add_palue to plot the p-threshold between different groups.
• Added embedding_multi to support the mudata object
• Added purple_color to visualize the purple palette.
• Added venn to plot the venn from set 2 to set 4
• Added boxplot to visualize the boxdotplot
• Added volcano to visualzize the result of differential expressed genes

v 1.5.9¶

single Module¶

• Added slingshot in single.TrajInfer
• Fixed some error of scLTNN
• Added GPU mode to preprocess the data
• Added cNMF to calculate the nmf

space Module¶

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

v 1.6.0¶

Move CEFCON,GNTD,mofapy2,spaceflow,spatrio,STAligner,tosica from root to externel module.

space Module¶

• Added STT in omicverse.space to calculate the spatial transition tensor.
• Added scSLAT in omicverse.externel to align of different spatial slices.
• Added PROST in omicverse.externel and svg in omicverse.space to identify the spatially variable genes and domain.

single Module¶

• Added get_results_rfc in omicverse.single.cNMF to predict the precise cluster in complex scRNA-seq/stRNA-seq
• Added get_results_rfc in omicverse.utils.LDA_topic to predict the precise cluster in complex scRNA-seq/stRNA-seq
• Added gptcelltype in omicverse.single to annotate celltype using large language model #82.

pl Module¶

• Added plot_spatial in omicverse.pl to visual the spot proportion of cells when deconvolution

v 1.6.2¶

Support Raw Windows platform

• Added mde in omicverse.pp to accerate the umap calculation.

v 1.6.3¶

• Added ov.setting.cpu_init to change the environment to CPU.
• Move module tape,SEACells and palantir to externel

Single Module¶

• Added CytoTrace2 to predict cellular potency categories and absolute developmental potential from single-cell RNA-sequencing data.
• Added cpdb_exact_target and cpdb_exact_source to exact the means of special ligand/receptor
• Added gptcelltype_local to identify the celltype using local LLM #96 #99

Bulk Module¶

• Added MaxBaseMean columns in dds.result to help people ignore the empty samples.

Space Module¶

• Added **kwargs in STT.compute_pathway
• Added GraphST to identify the spatial domain

pl Module¶

• Added cpdb_network, cpdb_chord, cpdb_heatmap, cpdb_interacting_network,cpdb_interacting_heatmap and cpdb_group_heatmap to visualize the result of CellPhoneDB

utils Module¶

• Added mclust_py to identify the Gaussian Mixture cluster
• Added mclust methdo in cluster function

v 1.6.4¶

Bulk Module¶

• Optimised pyGSEA's geneset_plot visualisation of coordinate effects
• Fixed an error of pyTCGA.survival_analysis when the matrix is sparse. #62, #68, #95
• Added tqdm to visualize the process of pyTCGA.survial_analysis_all
• Fixed an error of data_drop_duplicates_index with remove duplicate indexes to retain only the highest expressed genes #45
• Added geneset_plot_multi in ov.bulk to visualize the multi results of enrichment. #103

Single Module¶

• Added mellon_density to calculate the cell density. #103

PP Module¶

• Fixed an error of ov.pp.pca when pcs smaller than 13. #102
• Added COMPOSITE in ov.pp.qc's method to predicted doublet cells. #103
• Added species argument in score_genes_cell_cycle to calculate the cell phase without gene manual input

v 1.6.6¶

Pl Module¶

• Fixed the 'celltyep_key' error of ov.pl.cpdb_group_heatmap #109
• Fixed an error in ov.utils.roe when some expected frequencies are less than expected value.
• Added cellstackarea to visual the Percent stacked area chart of celltype in samples.

Single Module¶

• Fixed the bug of ov.single.cytotrace2 when adata.X is not sparse data. #115, #116
• Fixed the groupby error in ov.single.get_obs_value of SEACells.
• Fixed the error of cNMF #107, #85
• Fixed the plot error when Pycomplexheatmap version > 1.7 #136

Bulk Module¶

• Fixed an key error in ov.bulk.Matrix_ID_mapping
• Added enrichment_multi_concat in ov.bulk to concat the result of enrichment.
• Fixed the pandas version error in gseapy #137

Bulk2Single Module¶

• Added adata.var_names_make_unique() to avoid mat shape error if gene not unique. #100

Space Module¶

• Fixed an error in construct_landscape of ov.space.STT
• Fixed an error of get_image_idx_1D in ov.space.svg #117
• Added COMMOT to calculate the cell-cell interaction of spatial RNA-seq.
• Added starfysh to deconvolute spatial transcriptomic without scRNA-seq (#108)

PP Module¶

• Updated constraint error of ov.pp.mde #129
• Fixed type error of float128 #134

v 1.6.7¶

Space Module¶

• Added n_jobs argument to adjust thread in extenel.STT.pl.plot_tensor_single
• Fixed an error in extenel.STT.tl.construct_landscape
• Updated the tutorial of COMMOT and Flowsig

Pl Module¶

• Added legend_awargs to adjust the legend set in pl.cellstackarea and pl.cellproportion

Single Module¶

• Fixed the error of get_results and get_results_rfc in cNMF module. (#143) (#139)
• Added sccaf to obtain the best clusters.
• Fixed the .str error in cytotrace2 (#146)

Bulk Module¶

• Fixed the import error of gseapy in bulk.geneset_enrichment
• Optimized code logic for offline enrichment analysis, added background parameter
• Added pyWGCNA package replace the raw calculation of pyWGCNA (#162)

Bulk2Single Module¶

• Remove _stat_axis in bulk2single_data_prepare and use index instead of it (#160).

PP Module¶

• Fixed a return bugs in pp.regress_and_scale (#156)
• Fixed a scanpy version error when using ov.pp.pca (#154)

v 1.6.8¶

Bulk Module¶

• Fixed the error of log_init in gsea_obj.enrichment (#184)
• Added ax argument to visualize the geneset_plot

Space Module¶

• Added CAST to integrate multi slice
• Added crop_space_visium in omicverse.tl to crop the sub area of space data

Pl Module¶

• Added legend argument to visualize the cpdb_heatmap
• Added text_show argument to visualize the cellstackarea
• Added ForbiddenCity color system

v 1.6.9¶

PP Module¶

• Added recover_counts to recover counts after ov.pp.preprocess
• removed the lognorm layers added in ov.pp.pca

Single Module¶

• Added MultiMap module to integrate multi species
• Added CellVote to vote the best cells
• Added CellANOVA to integrate samples and correct the batch effect
• Added StaVia to calculate the pseudotime and infer trajectory.

Space Module¶

• Added ov.space.cluster to identify the spatial domain
• Added Binary for spatial cluster
• Added Spateo to calculate the SVG

v 1.7.0¶

Added cpu-gpu-mixed to accelerate the analysis of scrna-seq using GPU. Changed the logo presentation of Omicverse to ov.plot_set

Bulk Module¶

• Added limma, edgeR in different expression gene analysis. (#238)
• Fixed the version error of DEseq2 analysis.

Single Module¶

• Added lazy function to calculate all function of scrna-seq (#291)
• Added generate_scRNA_report and generate_reference_table to generate the report and reference (#291) (#292)
• Fixed geneset_prepare not being able to read gmt not split by \t\t (#235) (#238)
• Added geneset_aucell_tmp,pathway_aucell_tmp,pathway_aucell_enrichment_tmp to test the chunk_size (#238)
• Added data enhancement of Fate
• Added plot_atlas_view_ov in VIA
• Fixed an error when the matrix is too large in recover_counts.
• Added forceatlas2 to calculate the X_force_directed.
• Added milo and scCODA to analysis different celltype abundance.
• Added memento to analysis different gene expression.

Space Module¶

• Added GASTON to learn a topographic map of a tissue slice from spatially resolved transcriptomics (SRT) data (#238)
• Added super kwargs in plot_tensor_single of STT.
• Updated COMMOT using GPU-accerlate

Plot Module¶

• Added dotplot_doublegroup to visual the genes in doublegroup.
• Added transpose argument of cpdb_interacting_heatmap to transpose the figure.
• Added calculate_gene_density to plot the gene's density.

v 1.7.1¶

Single Module¶

• Fixed some error of ov.single.lazy.
• Fixed the format of ov.single.generate_scRNA_report
• Updated some functions of palantir
• Added CellOntologyMapper to map cell name.

v 1.7.2¶

Pl Module¶

• Optimated the plot effect of ov.pl.box_plot
• Optimated the plot effect of ov.pl.volcano Optimated the plot effect of ov.pl.violin
• Added beautiful dotplot than scanpy (#318)
• Added the similar visualization function of CellChat. (#313)

Space Module¶

• Added 3D cell-cell interaction analysis in COMMOT (#315)

Single Module¶

• Fixed the error of pathway_enrichment. (#184)
• Added SCENIC module with GPU-accerlate. (#331)

utils Module¶

• Added scICE to calculate the best cluster (#329)