Files in juliendelile/Antler
ANother Transcriptome Lineage ExploreR
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/.gitignore
R/carver.R
R/carver_functions.R
R/cell_clusters.R
R/cell_state_graph.R
R/cell_state_graph_functions.R
R/gene_modules.R
R/gene_modules_functions.R
R/main.R
R/plot_functions.R
R/pseudotime_functions.R
R/utils_functions.R
R/zzz.R
README.md
_pkgdown.yml
docs/404.html
docs/LICENSE-text.html
docs/apple-touch-icon-120x120.png
docs/apple-touch-icon-152x152.png
docs/apple-touch-icon-180x180.png
docs/apple-touch-icon-60x60.png
docs/apple-touch-icon-76x76.png
docs/apple-touch-icon.png
docs/articles/Carving-cell-trajectories.html
docs/articles/Transcriptomic-summary.html
docs/articles/images/Cell_clustering_heuristic_hclust.png
docs/articles/images/Cell_state_graph_kNN_gephiForceAtlas2_timepoint-hclust-lin10g01.png
docs/articles/images/Cell_state_graph_kNN_gephiForceAtlas2_timepoint-lin10g01-lin10g01.png
docs/articles/images/Cell_state_graph_kNN_gephiForceAtlas2_timepoint.png
docs/articles/images/Compact_dataset.png
docs/articles/images/Gene_module_identification_unbiasedGMs_heuristic_loop_0.png
docs/articles/images/Optimization_Pareto_progression.png
docs/articles/images/PT_dynamics_lin09g01_Normalized.png
docs/articles/images/PT_tree_cell_state_graph_landmarks.png
docs/articles/images/PT_tree_cell_state_graph_pt.png
docs/articles/images/PT_tree_communities.png
docs/articles/images/PT_tree_pt.png
docs/articles/images/SA_history.png
docs/articles/images/Top_Final_cluster_MST_graphs.png
docs/articles/images/Transcriptome_summary_selection_I_hclust_selection_I_Normalized_logscaled.png
docs/articles/images/Transcriptome_summary_unbiasedGMs_hclust_Normalized_logscaled.png
docs/articles/images/Transcriptome_summary_unbiased_gms_hclust_Normalized_logscaled.png
docs/articles/images/Transcriptome_summary_unbiased_gms_hclust_Smoothed_logscaled.png
docs/articles/images/candidate_kernel_params.png
docs/articles/images/carvings_SA_cell_state_graph.png
docs/articles/images/cell_count_by_timepoint.png
docs/articles/images/expressed_genes_count_by_timepoint.png
docs/articles/images/expressed_genes_per_cell.png
docs/articles/images/library_sizes.png
docs/articles/images/library_sizes_II_by_timepoint.png
docs/articles/images/library_sizes_I_by_timepoint.png
docs/articles/images_ext/Transcriptome_summary_unbiasedGMs_hclust_Normalized_logscaled.cairo.png
docs/articles/images_ext/carving_intro.png
docs/articles/images_ext/carving_schematic.png
docs/articles/images_ext/gene_module_identification.png
docs/articles/images_ext/synthetic_schematic.png
docs/articles/index.html
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/favicon-16x16.png
docs/favicon-32x32.png
docs/favicon.ico
docs/index.html
docs/link.svg
docs/logo.png
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/Antler-class.html
docs/reference/add_color_map.html
docs/reference/brew_more_colors.html
docs/reference/build_pseudotime_tree.html
docs/reference/carve.html
docs/reference/cell_clusters_identify.html
docs/reference/cell_names.html
docs/reference/cell_state_graph_plot.html
docs/reference/convert_ensembl_id_to_name.html
docs/reference/define_cell_samples.html
docs/reference/dispersed_genes.html
docs/reference/exclude_exotic_genes.html
docs/reference/exclude_unexpressed_genes.html
docs/reference/export_expressionset.html
docs/reference/gene_modules_export.html
docs/reference/gene_modules_identify.html
docs/reference/gene_modules_report_genes.html
docs/reference/gene_modules_select_from_gene_names.html
docs/reference/gene_modules_select_from_ids.html
docs/reference/gene_names.html
docs/reference/genes_from_GOterms.html
docs/reference/index.html
docs/reference/load_dataset.html
docs/reference/normalize.html
docs/reference/num_cells.html
docs/reference/num_genes.html
docs/reference/plot_QC.html
docs/reference/plot_pseudotime_dynamics.html
docs/reference/plot_transcriptome_summary.html
docs/reference/read_counts.html
docs/reference/remove_cells.html
docs/reference/remove_clusters.html
docs/reference/remove_genes.html
docs/reference/remove_outliers.html
docs/reference/report.html
docs/reference/sample_size.html
docs/reference/save_dataset.html
docs/reference/select_dispersed_genes.html
docs/reference/set_favorite_genes.html
docs/reference/smooth.html
docs/reference/test_kernel_widths.html
inst/extdata/Annotations/biomart_ensemblid_genename_ggallus.csv
inst/extdata/Annotations/biomart_ensemblid_genename_mmusculus.csv
inst/extdata/Annotations/gene_goterms.txt
inst/extdata/mouse_spinal_cord/assayData.csv
inst/extdata/mouse_spinal_cord/phenoData.csv
inst/extdata/synthetic_lineage/assayData.csv
inst/extdata/synthetic_lineage/phenoData.csv
inst/extdata/synthetic_lineage/settings.json
inst/java/LayoutGephi.jar
inst/java/lib/gephi-toolkit-0.9.2-all.jar
logo.png
man/Antler-class.Rd
man/add_color_map.Rd
man/brew_more_colors.Rd
man/build_pseudotime_tree.Rd
man/carve.Rd
man/cell_clusters_identify.Rd
man/cell_names.Rd
man/cell_state_graph_plot.Rd
man/convert_ensembl_id_to_name.Rd
man/define_cell_samples.Rd
man/dispersed_genes.Rd
man/exclude_exotic_genes.Rd
man/exclude_unexpressed_genes.Rd
man/export_expressionset.Rd
man/gene_modules_export.Rd
man/gene_modules_identify.Rd
man/gene_modules_report_genes.Rd
man/gene_modules_select_from_gene_names.Rd
man/gene_modules_select_from_ids.Rd
man/gene_names.Rd
man/genes_from_GOterms.Rd
man/load_dataset.Rd
man/normalize.Rd
man/num_cells.Rd
man/num_genes.Rd
man/plot_QC.Rd
man/plot_pseudotime_dynamics.Rd
man/plot_transcriptome_summary.Rd
man/read_counts.Rd
man/remove_cells.Rd
man/remove_clusters.Rd
man/remove_genes.Rd
man/remove_outliers.Rd
man/report.Rd
man/sample_size.Rd
man/save_dataset.Rd
man/select_dispersed_genes.Rd
man/set_favorite_genes.Rd
man/smooth.Rd
man/test_kernel_widths.Rd
pkgdown/favicon/apple-touch-icon-120x120.png
pkgdown/favicon/apple-touch-icon-152x152.png
pkgdown/favicon/apple-touch-icon-180x180.png
pkgdown/favicon/apple-touch-icon-60x60.png
pkgdown/favicon/apple-touch-icon-76x76.png
pkgdown/favicon/apple-touch-icon.png
pkgdown/favicon/favicon-16x16.png
pkgdown/favicon/favicon-32x32.png
pkgdown/favicon/favicon.ico
vignettes/.gitignore
vignettes/Carving-cell-trajectories.Rmd
vignettes/Transcriptomic-summary.Rmd
vignettes/images/Cell_clustering_heuristic_hclust.png
vignettes/images/Cell_state_graph_kNN_gephiForceAtlas2_timepoint-hclust-lin10g01.png
vignettes/images/Cell_state_graph_kNN_gephiForceAtlas2_timepoint-lin10g01-lin10g01.png
vignettes/images/Cell_state_graph_kNN_gephiForceAtlas2_timepoint.png
vignettes/images/Compact_dataset.png
vignettes/images/Gene_module_identification_unbiasedGMs_heuristic_loop_0.png
vignettes/images/Optimization_Pareto_progression.png
vignettes/images/PT_dynamics_lin09g01_Normalized.png
vignettes/images/PT_tree_cell_state_graph_landmarks.png
vignettes/images/PT_tree_cell_state_graph_pt.png
vignettes/images/PT_tree_communities.png
vignettes/images/PT_tree_pt.png
vignettes/images/SA_history.png
vignettes/images/Top_Final_cluster_MST_graphs.png
vignettes/images/Transcriptome_summary_selection_I_hclust_selection_I_Normalized_logscaled.png
vignettes/images/Transcriptome_summary_unbiasedGMs_hclust_Normalized_logscaled.png
vignettes/images/Transcriptome_summary_unbiased_gms_hclust_Normalized_logscaled.png
vignettes/images/Transcriptome_summary_unbiased_gms_hclust_Smoothed_logscaled.png
vignettes/images/candidate_kernel_params.png
vignettes/images/carvings_SA_cell_state_graph.png
vignettes/images/cell_count_by_timepoint.png
vignettes/images/expressed_genes_count_by_timepoint.png
vignettes/images/expressed_genes_per_cell.png
vignettes/images/library_sizes.png
vignettes/images/library_sizes_II_by_timepoint.png
vignettes/images/library_sizes_I_by_timepoint.png
vignettes/images_ext/Transcriptome_summary_unbiasedGMs_hclust_Normalized_logscaled.cairo.png
vignettes/images_ext/carving_intro.png
vignettes/images_ext/carving_schematic.png
vignettes/images_ext/gene_module_identification.png
vignettes/images_ext/synthetic_schematic.png
vignettes/script/Carving_dataset.py
