- Fix NAMESPACE (xlxs dependency).
- Rebuilt doc in html format.
- Remove xlxs dependency in favor with WriteXLS dependency (to avoid rJava dependency).
- Fix an issue with temp dir.
-
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().
- Prefix version with a v...
- keep_nn argument is deprecated (
gene_clustering()).
- Fix #134
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Remove DynmicTreeCut dependency.
-
Fix bug #137.
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Added color for cell cluster in
plot_ggheatmap(). -
Updated doc.
-
Minor bug fix.
-
Updated doc
- 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()andplot_cluster_stats()to perform statistics on clusters. - Added export:
cluster_set_to_xls(). - Added
compare_genesets()andplot_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.
- 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
- 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)
- 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
- 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.
- 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.
- 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
- Scigenex now depends on R 4.0.0
- No more reference to Biobase in the code.
- Fix call to MCL.
- Now provides a support for R MCL library (not recommended).
-
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().
- Several code changes which were not clearly traced at the moment... Sry.