v1.6.9

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

v1.6.8

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

v1.6.7

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)

v1.6.6

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

v1.6.4

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

v1.6.3

• 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

What's Changed

• Add a function of cell types annotation with local LLMs by @fredsamhaak in #96
• Add guidance on using local LLMs for cell types annotation by @fredsamhaak in #99

New Contributors

• @fredsamhaak made their first contribution in #96

Full Changelog: v1.6.2...v1.6.3

v1.6.2

Supports native windows platform, no need to install additional wsl subsystem, but note that some features may not be fully supported under windows platform, such as pyVIA, pybedtools, etc.

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

v1.6.0

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

v1.5.9

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

v1.5.8

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