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

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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

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docs/favicon.ico

docs/index.html

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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

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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

juliendelile/Antler documentation built on June 19, 2021, 9 a.m.