changelog.md

In dputhier/scigenex: The scigenex package (Single-Cell Informative GENe Explorer)

Changelog

v1.5.0

• Added support for Louvain and walktrap: call_walktrap_clusterset(), call_louvain_clusterset()
• construct_new_graph() was renamed do_closest_neighbor_graph()
• keep_dbf_graph() was renamed do_reciprocal_neighbor_graph()
• code refactoring (mainly comments).

v1.4.10

• Fix NAMESPACE (xlxs dependency).
• Rebuilt doc in html format.

v1.4.9

• Remove xlxs dependency in favor with WriteXLS dependency (to avoid rJava dependency).

v1.4.8

• Fix an issue with temp dir.

v1.4.7

• Change k_g argument to 's' in gene_clustering() function for clarity purpose.

• Added dependency to DT library (required by cluster_set_report()).

• Updated html doc.

• Fix an issue with pandoc in clusterset_report().

• Improved importfrom in clusterset_report().

v1.4.6

• Prefix version with a v...

v1.4.5

• keep_nn argument is deprecated (gene_clustering()).

v1.4.4

• Fix #134

v1.4.3

• Remove DynmicTreeCut dependency.

• Fix bug #137.

v1.4.2

• Added color for cell cluster in plot_ggheatmap().

• Updated doc.

v1.4.1

• Minor bug fix.

• Updated doc

v1.4.0

• Update of the documentation
• Added support for spatial transcriptomics: getFlippedTissueCoordinates(), plot_spatial(), plot_spatial_panel().
• Added import from matrix and Seurat object: cluster_set_from_matrix(), cluster_set_from_seurat().
• Added cluster_stats() and plot_cluster_stats() to perform statistics on clusters.
• Added export: cluster_set_to_xls().
• Added compare_genesets() and plot_cmp_genesets() to compare gene lists with various statistics.
• Added plot_clust_enrichments() to compare functional enrichment over clusters.
• Added plot_ggheatmap() for statically display heatmaps.
• Added plot_markers_to_clusters() to map markers onto clusters.
• Added top_by_go() to select top genes by GO terms.

v1.3.1

• Update of the documentation
• Improve get_genes function : gene names are ordered by gene clusters
• Fix viz_enrich function : viz_enrich function is now working when using a specific ontology db as ontology parameter in enrich_go function

v1.3.0

• Add a clustering method using hierchical clustering and DynamicTreeCut R package
• Add a cell_clusters slot in the ClusterSet object
• Create a new documentation
• Modification of the av_dot_prod_min filter : use the max of the median values of the dot product
• Add get_genes and get_cells functions
• Improve the computational speed of DBFMCL function
• Replace the name of the slot "cluster" by "gene_patterns"
• Implementation of new test (testthat)

v1.2.21

• Update the package used for enrichment analysis to use ClusterProfiler
• Update visualization of enrichment analysis results : add dotplot and barplot provided by ClusterProfiler
• Add more parameters to control the density plot of distances
• Fix issues from Github

v1.2.2

• Replace the C code for DBF function by a R implementation to reduce the computational time.
• Split the main R script into sub-script related to each function of scigenex package.

v1.1.2

• Create plot_heatmap function to generate an interactive heatmap of the gene clusters
• Modify NAMESPACE and DESCRIPTION file and add import_package.R files to automatically update dependencies using roxygen2::roxygenise()
• Create top_genes function to find the top n genes from each signature. This function is also usefull for the plot_heatmap function.
• Add a slot in the ClusterSet object containing the filename of the output file including simulated distances and cutting threshold.
• Modify the input of plot_dist function to a ClusterSet object.
• Update enric_analysis function : run the functional enrichment analysis for each gene cluster.
• Remove R implementation of MCL. The package used is no more maintained and the released version needs to be fixed.

v1.0.2

• Fix fprint_selected function in C code byt changing type of len varibale to size_t
• Set default optional_output parameter of DBF and DBFMCL function to TRUE

v1.0.1

Bug Fixes

API/CLI Changes

• Scigenex now depends on R 4.0.0
• No more reference to Biobase in the code.

Code changes

New Features

v0.1.7

Bug Fixes

• Fix call to MCL.

API/CLI Changes

Code changes

New Features

v0.1.6

Bug Fixes

API/CLI Changes

• Now provides a support for R MCL library (not recommended).

Code changes

New Features

v0.1.4

Bug Fixes

API/CLI Changes

• The DBFMCLresult object has been replaced by a more versatile object: ClusterSet.

• The plot_dbf() method has been replaced by plot_clust().

• The write_dbf() method has been replaced by write_clust().

Code changes

• Several code changes which were not clearly traced at the moment... Sry.

New Features

dputhier/scigenex documentation built on Dec. 24, 2024, 4:38 p.m.