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changelog.md

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Changelog

  • Aded coord_flip argument to plot_ggheatmap()
  • Added top_by_grep()

v1.5.2

  • Added as_list argument to grep_clust().
  • Added single_file to write_clust().
  • Added to_lin to plot_profile.
  • Deleted dot_prod from cluster_stats() and added CV.
  • Added top_by_intersect().

v1.5.1

  • Fix gene_clustering() and mcl_install(). Added 'mcl_dir' argument to gene_clustering() (in case automated installation in difficult, e.g., when running in a proprietary environnement).
  • Fix top_by_go(). Added argument 'as_list'.
  • Documentation has been splitted in two part (scRNA-seq and ST).

v1.4.13

  • 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).
  • Deleted code relics (ident argument as list) from plot_ggheatmap().
  • Added the subsample_by_ident() method for a ClusterSet object. handy to be used with plot_ggheatmap or plot_heatmap (to put emphasis on small populations).
  • Added grep_clust() to search for genes in a ClusterSet object using a REGEXP.
  • Added reload_pac() (for development).

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