Changelog

0.7.0 (23-04-24)

• Added code examples for tools and utils (#140)

  • recluster

  • group_heatmap

  • plot_venn

  • in_range

• Fix notebooks in readthedocs documentation (#220)

• Removed custom_marker_annotation script

• Disintegrated FLD scoring and added PEAKQC to setup.py (#233)

• fixed PCA-var plot not fitting into anndata_overview (#232)

Changes to notebooks

• Overhaul RNA & ATAC notebooks structure (includes #207)

• Revise RNA notebook 4 recluster section (#201)

0.6.1 (28-03-24)

• Fix release pages by renaming the release-pages: job to pages:

• refactor move clean-orphaned-tags to new stage .post (#229)

0.6 (27-03-24)

• Fix unable to determine R_HOME error (#190)

• implemented propose_pcs to automatically select PCA components (#187)

• add correlation barplot to plot_pca_variance

• created correlation_matrix method by restructuring plot_pca_correlation

• Fix beartype issue with Lists and Iterables containing Literals (#227)

• CICD overhaul (#191)

• fixed notebook version in the env to 6.5.2 (#199, partly #44)

Changes to notebooks

• Move proportion_analysis notebooks to general notebooks (#195 and #214)

• replace scanpy pseudotime with scFates in pseudotime_analysis notebook

• prepare_for_cellxgene: Adapt to new mampok verison 2.0.9

• prepare_for_cellxgene: Allows the user to set an analyst manually (#213)

• rna 03_batch revision (#209, #202, #200, #152)

• 05_marker_genes: Complete Overhaul (#181)

0.5 (04-03-24)

• add receptor_genes & ligand_genes parameters to connectionPlot and decreased runtime

• readme update(#188)

• Fix error when writing adata converted from an R object (#205, #180)

• Marker Repo integration (#162)

• Set scvelo version to >=0.3.1 (#193)

• Added fa2 as dependency for pseudotime analysis

• anndata_overview: fix issue where colorbars for continuous data was not shown

• added ability to use highly variable features using the lsi() function (#165)

• removed deprecated group_heatmap, umap_pub (replaced by gene_expression_heatmap, plot_embedding)

• add doku page

• start change log

Changes to notebooks

• rna assembly: refactor

• prepare_for_cellxgene: Added BN_public as possible deployment cluster (#192)

• 14_velocity_analysis: Remove duplicate parameter (#194)

• pseudotime_analysis: Save generated plots (#211)

• rna 03_batch: added qc metrics to overview plot

0.4 (31-1-24)

• Fix get_rank_genes_tables for groups without marker genes (#179)

• Bugfixes for CI jobs

• Fix check_changes pipeline

• Fix typos (#173 & #174)

• Include kwargs in utils.bioutils._overlap_two_bedfiles(#177)

• Implemented _add_path() to automatically add python path to environment

• added tests for _add_path() and _overlap_two_bedfiles() (#177)

• constraint ipywidgets version to 7.7.5 to fix the quality_violinplot() (#151)(#143)

• Add temp_dir to calc_overlap_fc.py (#167) and revised related functions

• more testing (mainly sctoolbox.tools) (#166)

• gerneral text revisions

Changes to notebooks

• Add pseudotime & velocity analysis notebooks (#164)

• Update receptor-ligand notebook (#176)

• Refactored annotate_genes() from ATAC-notebook 05 to 04 and removed 05 (#175)

0.3 (30-11-2023)

• Add parameter type hinting including runtime type checking (#46)

• Fixed prepare_for_cellxgene color issue (#145, #146)

• Add CI/CD container build pipeline for testing (#135)

• Fixed example for gene_expression_heatmap and smaller bugfixes related to marker genes (#124)

• Removed pl.group_heatmap as it is fully covered by pl.gene_expression_heatmap

• Removed ‘sinto’ as dependency and added code in ‘create_fragment_file’ to create fragment file internally (solves #147)

• The function ‘create_fragment_file’ was moved to bam tools.

• Added “n_genes” parameter to tools.marker_genes.get_rank_genes_tables, and set the default to 200 (#153)

• Fixed CI/CD build job rules. Only trigger build job when files changed or triggered manually

• Add parameter to plot_pca_correlation to plot correlation with UMAP components (#157)

• Handle NaN values for plot_pca_correlation (#156)

• implemented prepare_for_cellxgene

• Added pl.embedding.plot_embedding() function to plot embeddings with different styles, e.g. hexbin and density (#149)

• Modified pl.embedding.plot_embedding() to plot different embedding dimensions

• Deprecated pl.umap_pub as this is now covered by pl.plot_embedding

• changed typing to beartype.typing

• Added GenomeTracks plotting

• Fix batch evaluation for small datasets (#148)

• Added **kwargs to functions which are wrappers for other functions

• added RAGI cluster validation to clustering.py (!201)

• started disintegrating fld scoring (!201)

• reorganised ATAC-notebooks (!201)

Changes to notebooks

• Added prepare for cellxgene notebook (#139)

• Added plot of highly expressed genes to RNA notebook 03 (#43)

• Changed structure of notebooks in directory; added “notebooks” subdirectories for RNA and ATAC

0.2 (30-08-2023)

• fix error in prepare_for_cellxgene caused by .uns[_color] not matching .obs column. (#176)

• implemented prepare_for_cellxgene (#147)

• fixed raw value copy issue in rna/02-batch notebook

• Added parameters for the TOBIAS flags in the config file to write_TOBIAS_config()

• Added logging verbose and decorator to ATAC related functions

• Fix “shell not found” error for CI pipeline (#129)

• Pinned scikit-learn to version <=1.2.2 (#128)

• Added script for gene correlation and comparison between two conditions

• Added check for marker gene lists (#103)

• Keep notebook metadata on push to prevent deleting kernel information

• Added sctoolbox as default kernel to RNA & ATAC notebooks

• Added check of column validity to tools.marker_genes.run_DESeq2() (#134)

• Increase test coverage for plotting functions (#126)

• Apply fixes to bugs found by increasing the test coverage.

• Added type hinting to functions.

• Revised doc-strings.

• run_rank_genes() auto converts groupby column to type ‘category’ (#137)

• Fix parameter for gene/cell filtering (#136)

• Add Check to _filter_object() if column contains only boolean (#110)

• Add support of matrx and numpy.ndarray type of adata.X for predict_sex (#111)

• Add method to get pd.DataFrame columns with list of regex (#90)

• Added ‘pairwise_scatter’ method for plotting QC metrics (#54)

• Add ATAC quality metrics TSSe (ENCODE), FRiP

• Revised FLD density plotting

• Adjusted style of default values in docs (#33)

• Added ‘plot_pca_correlation’ for plotting PCA correlation with obs/var columns (#118)

• Removed outdated normalization methods.

• Changed all line endings to LF (#138)

• Disabled threads parameter for tSNE (#130)

• Added ‘plot_starsolo_quality’ and ‘plot_starsolo_UMI’ to plotting module (#78)

• Fixed issues with clustered dotplot with new code (#122)

Changes to RNA notebooks

• Added display of 3D UMAP html in notebook 04 (#119)

Changes to ATAC notebooks

• Fixed assembling atac notebook 01

• Fixed get_atac_thresholds_wrapper and renamed it to get_thresholds_wrapper

• Added custome cwt implementation

• Added additional parameters to add_insertsize_metrics

• Revised nucleosomal score scoring

0.1.1 (24-05-2023)

• Fixed import issue

• Make version accessible

• Added check for CHANGES.rst in gitlab-ci

• Pinned numba==0.57.0rc1 due to import error (#117)

• Fixed bug in tools.norm_correct.atac_norm

• Added check for sctoolbox/_version.py file in gitlab-ci

0.1 (22-05-2023)

• First version