Files in whtns/seuratTools

Tools for Managing Seurat Objects

.DS_Store

.Rbuildignore

.Renviron

.Rprofile

.dockerignore

.gitignore

.here

.travis.yml

DESCRIPTION

Dockerfile

LICENSE

LICENSE.md

NAMESPACE

NEWS.md R/cellalign.R R/create_seu.R R/cross_species.R R/custom_ui.R R/data.R R/data_edit.R R/docker_app.R R/enrichment.R

R/generics.R

R/minimal_app.R R/misc.R R/monocle.R R/monocle2.R R/pipeline.R R/plotting.R R/project_management.R R/regress_features.R R/run_scvelo.R R/seuratTools-package.R R/seurat_annotation.R R/seurat_app.R R/seurat_cluster.R R/seurat_integrate.R R/seurat_reference_integrate.R R/shiny_modules.R R/update_child_exp_metadata.R R/update_seurat_from_child_metadata.R R/utils-pipe.R R/utils.R R/velocyto.R R/wiggleplotr.R R/workflow.R R/zzz.R README.Rmd README.md

README.orig

README_cache/gfm/__packages

README_cache/gfm/unnamed-chunk-14_b30d14d5cd2049f0015424d434425790.RData

README_cache/gfm/unnamed-chunk-14_b30d14d5cd2049f0015424d434425790.rdb

README_cache/gfm/unnamed-chunk-14_b30d14d5cd2049f0015424d434425790.rdx

README_cache/gfm/unnamed-chunk-20_77d500b0f4cf5302be5f78946080ec2f.RData

README_cache/gfm/unnamed-chunk-20_77d500b0f4cf5302be5f78946080ec2f.rdb

README_cache/gfm/unnamed-chunk-20_77d500b0f4cf5302be5f78946080ec2f.rdx

README_cache/gfm/unnamed-chunk-21_5ae6930f7347a291056003e827a22dbb.RData

README_cache/gfm/unnamed-chunk-21_5ae6930f7347a291056003e827a22dbb.rdb

README_cache/gfm/unnamed-chunk-21_5ae6930f7347a291056003e827a22dbb.rdx

README_cache/gfm/unnamed-chunk-5_bb88e840a5c31919f5d84549120d1da5.RData

README_cache/gfm/unnamed-chunk-5_bb88e840a5c31919f5d84549120d1da5.rdb

README_cache/gfm/unnamed-chunk-5_bb88e840a5c31919f5d84549120d1da5.rdx

README_docs/add_arbitrary_metadata.gif

README_docs/subset_by_csv.gif

_pkgdown.yml

data-raw/human_to_mouse_homologs.R

data/baron2016singlecell.rda

data/cc.genes.rda

data/celltype_markers.rda

data/go.gs.rda

data/hsa.grn.rda

data/human_count.rda

data/human_gene_transcript_seu.rda

data/human_meta.rda

data/human_to_mouse_homologs.rda

data/kegg.gs.rda

data/mito_features.rda

data/monocle_cds.rda

data/msigdb.gs.rda

data/panc8.rda

data/panc8_count_mat.rda

data/panc8_metadata.rda

data/pseudogenes.rda

data/ribo_features.rda

docs/404.html

docs/LICENSE-text.html

docs/LICENSE.html

docs/articles/Heatmap2.0.PNG

docs/articles/Heatmap2.0.png

docs/articles/PlotCoverage2.0.PNG

docs/articles/PlotCoverage2.0.png

docs/articles/Screenshot 2023-08-25 at 1.28.26 PM.png

docs/articles/Screenshot 2023-08-25 at 1.40.35 PM.png

docs/articles/Screenshot 2023-08-25 at 1.40.57 PM.png

docs/articles/Screenshot_2023-08-25_at_1.28.26_PM.png

docs/articles/Screenshot_2023-08-25_at_1.40.35_PM.png

docs/articles/Screenshot_2023-08-25_at_1.40.57_PM.png

docs/articles/clustree.png

docs/articles/images/Heatmap2.0.PNG

docs/articles/images/Heatmap2.0.png

docs/articles/images/PlotCoverage2.0.PNG

docs/articles/images/PlotCoverage2.0.png

docs/articles/images/Screenshot 2023-08-25 at 1.28.26 PM.png

docs/articles/images/Screenshot 2023-08-25 at 1.40.35 PM.png

docs/articles/images/Screenshot 2023-08-25 at 1.40.57 PM.png

docs/articles/images/Screenshot_2023-08-25_at_1.28.26_PM.png

docs/articles/images/Screenshot_2023-08-25_at_1.40.35_PM.png

docs/articles/images/Screenshot_2023-08-25_at_1.40.57_PM.png

docs/articles/images/clustree.png

docs/articles/images/integration_image.png

docs/articles/images/louvain_and_feature_umap_plot.png

docs/articles/images/marker_gene_plot.png

docs/articles/images/monocle_final_steps.png

docs/articles/images/monocle_first_steps.png

docs/articles/images/pair_of_histograms.png

docs/articles/images/transcript_composisiont.png

docs/articles/images/unnamed-chunk-9-1.png

docs/articles/images/violinPlot.PNG

docs/articles/images/violinPlot.png

docs/articles/index.html

docs/articles/integration.html

docs/articles/integration_files/figure-html/unnamed-chunk-4-1.png

docs/articles/integration_files/figure-html/unnamed-chunk-5-1.png

docs/articles/louvain_and_feature_umap_plot.png

docs/articles/marker_gene_plot.png

docs/articles/monocle_final_steps.png

docs/articles/monocle_first_steps.png

docs/articles/pair_of_histograms.png

docs/articles/pipeline.html

docs/articles/preprocessing.html

docs/articles/preprocessing_files/figure-html/unnamed-chunk-14-1.png

docs/articles/preprocessing_files/figure-html/unnamed-chunk-16-1.png

docs/articles/preprocessing_files/figure-html/unnamed-chunk-17-1.png

docs/articles/preprocessing_files/figure-html/unnamed-chunk-18-1.png

docs/articles/preprocessing_files/figure-html/unnamed-chunk-4-1.png

docs/articles/preprocessing_files/figure-html/unnamed-chunk-5-1.png

docs/articles/preprocessing_files/figure-html/unnamed-chunk-6-1.png

docs/articles/preprocessing_files/kePrint-0.0.1/kePrint.js

docs/articles/preprocessing_files/lightable-0.0.1/lightable.css

docs/articles/shiny_app.html

docs/articles/transcript_composisiont.png

docs/articles/unnamed-chunk-9-1.png

docs/articles/violinPlot.PNG

docs/articles/violinPlot.png

docs/articles/visualization.html

docs/articles/visualization_files/figure-html/unnamed-chunk-10-1.png

docs/articles/visualization_files/figure-html/unnamed-chunk-11-1.png

docs/articles/visualization_files/figure-html/unnamed-chunk-11-2.png

docs/articles/visualization_files/figure-html/unnamed-chunk-12-1.png

docs/articles/visualization_files/figure-html/unnamed-chunk-12-2.png

docs/articles/visualization_files/figure-html/unnamed-chunk-12-3.png

docs/articles/visualization_files/figure-html/unnamed-chunk-12-4.png

docs/articles/visualization_files/figure-html/unnamed-chunk-3-1.png

docs/articles/visualization_files/figure-html/unnamed-chunk-4-1.png

docs/articles/visualization_files/figure-html/unnamed-chunk-5-1.png

docs/articles/visualization_files/figure-html/unnamed-chunk-6-1.png

docs/articles/visualization_files/figure-html/unnamed-chunk-7-1.png

docs/articles/visualization_files/figure-html/unnamed-chunk-8-1.png

docs/articles/visualization_files/figure-html/unnamed-chunk-9-1.png

docs/authors.html

docs/deps/bootstrap-5.1.3/bootstrap.bundle.min.js

docs/deps/bootstrap-5.1.3/bootstrap.bundle.min.js.map

docs/deps/bootstrap-5.1.3/bootstrap.min.css

docs/deps/bootstrap-5.2.2/bootstrap.bundle.min.js

docs/deps/bootstrap-5.2.2/bootstrap.bundle.min.js.map

docs/deps/bootstrap-5.2.2/bootstrap.min.css

docs/deps/data-deps.txt

docs/deps/jquery-3.6.0/jquery-3.6.0.js

docs/deps/jquery-3.6.0/jquery-3.6.0.min.js

docs/deps/jquery-3.6.0/jquery-3.6.0.min.map

docs/index.html

docs/link.svg

docs/news/index.html

docs/pkgdown.js

docs/pkgdown.yml

docs/reference/Monocle2_diffex.html

docs/reference/SetDefaultAssay.html

docs/reference/add_census_slot.html

docs/reference/add_percent_mito.html

docs/reference/add_read_count_col.html

docs/reference/allTranscripts.html

docs/reference/allTranscriptsui.html

docs/reference/annotate_cell_cycle.html

docs/reference/annotate_excluded.html

docs/reference/append_to_project_db.html

docs/reference/arrange_ptime_heatmaps.html

docs/reference/assign_clusters_to_cds.html

docs/reference/build_bigwig_db.html

docs/reference/by_row_corr_between_pt_heatmaps.html

docs/reference/calc_cor_across_heatmaps.html

docs/reference/calc_pseudotime_heatmap.html

docs/reference/ccScore.html

docs/reference/ccScoreui.html

docs/reference/cells_selected.html

docs/reference/celltype_markers.html

docs/reference/changeEmbedParams.html

docs/reference/changeEmbedParamsui.html

docs/reference/chevreulBox.html

docs/reference/clustering_workflow.html

docs/reference/combine_cols.html

docs/reference/combine_looms.html

docs/reference/convert_human_seu_to_mouse.html

docs/reference/convert_monoclev2_to_seuv3.html

docs/reference/convert_mouse_seu_to_human.html

docs/reference/convert_seu_list_to_multimodal.html

docs/reference/convert_seu_to_cds.html

docs/reference/convert_seuv3_to_monoclev2.html

docs/reference/convert_symbols_by_species.html

docs/reference/convert_to_h5ad.html

docs/reference/convert_v3_to_v5.html

docs/reference/create_proj_matrix.html

docs/reference/create_project_db.html

docs/reference/cross_check_heatmaps.html

docs/reference/cross_plot_vars.html

docs/reference/cross_species_integrate.html

docs/reference/default_helper.html

docs/reference/diffex.html

docs/reference/diffexui.html

docs/reference/dot-send_enrichr_query.html

docs/reference/dropdownButton.html

docs/reference/filter_low_rc_cells.html

docs/reference/filter_merged_seu.html

docs/reference/filter_merged_seus.html

docs/reference/filter_rows_to_top.html

docs/reference/findMarkers.html

docs/reference/findMarkersui.html

docs/reference/find_all_markers.html

docs/reference/flip_pseudotime.html

docs/reference/format_new_metadata.html

docs/reference/format_pathway_table.html

docs/reference/gene_test_plot.html

docs/reference/genes_to_transcripts.html

docs/reference/getEnrichedPathways.html

docs/reference/get_meta.html

docs/reference/get_transcripts_from_seu.html

docs/reference/global_cellalign.html

docs/reference/harmony_integrate.html

docs/reference/human_to_mouse_homologs.html

docs/reference/index.html

docs/reference/integrateProj.html

docs/reference/integrateProjui.html

docs/reference/integration_workflow.html

docs/reference/label_transfer.html

docs/reference/learn_graph_by_resolution.html

docs/reference/list_plot_types.html

docs/reference/load_bigwigs.html

docs/reference/load_counts_by_tximport.html

docs/reference/load_meta.html

docs/reference/load_seurat_from_proj.html

docs/reference/load_seurat_path.html

docs/reference/local_cellalign.html

docs/reference/make_bigwig_db.html

docs/reference/make_chevreul_clean_names.html

docs/reference/mem_str.html

docs/reference/merge_small_seus.html

docs/reference/metadata_from_batch.html

docs/reference/minimalSeuratApp.html

docs/reference/monocle.html

docs/reference/monocle_module_heatmap.html

docs/reference/monocleui.html

docs/reference/nil.html

docs/reference/pad_sample_files.html

docs/reference/pathwayEnrichment.html

docs/reference/pathwayEnrichmentui.html

docs/reference/pipe.html

docs/reference/plotClustree.html

docs/reference/plotClustree_UI.html

docs/reference/plotCoverage.html

docs/reference/plotCoverage_UI.html

docs/reference/plotDimRed.html

docs/reference/plotDimRedui.html

docs/reference/plotHeatmap.html

docs/reference/plotHeatmapui.html

docs/reference/plotReadCount.html

docs/reference/plotReadCountui.html

docs/reference/plotVelocity.html

docs/reference/plotVelocityui.html

docs/reference/plotViolin.html

docs/reference/plotViolinui.html

docs/reference/plot_all_ptimes.html

docs/reference/plot_all_transcripts.html

docs/reference/plot_cds.html

docs/reference/plot_cell_cycle_distribution.html

docs/reference/plot_cells.html

docs/reference/plot_feature.html

docs/reference/plot_feature_in_ref_query_ptime.html

docs/reference/plot_gene_coverage_by_var.html

docs/reference/plot_markers.html

docs/reference/plot_monocle_features.html

docs/reference/plot_multiple_branches_heatmap.html

docs/reference/plot_pseudotime.html

docs/reference/plot_pseudotime_heatmap.html

docs/reference/plot_readcount.html

docs/reference/plot_ridge.html

docs/reference/plot_scvelo.html

docs/reference/plot_transcript_composition.html

docs/reference/plot_var.html

docs/reference/plot_violin.html

docs/reference/plotly_settings.html

docs/reference/prep_armor_meta.html

docs/reference/prep_plot_genes_in_pseudotime.html

docs/reference/prep_scvelo.html

docs/reference/prep_slider_values.html

docs/reference/process_monocle_child.html

docs/reference/propagate_spreadsheet_changes.html

docs/reference/read_project_db.html

docs/reference/record_experiment_data.html

docs/reference/reference_integrate.html

docs/reference/reformatMetadataDR.html

docs/reference/reformatMetadataDRui.html

docs/reference/regress_by_features.html

docs/reference/reintegrate_seu.html

docs/reference/rename_from_x_notation.html

docs/reference/rename_seurat.html

docs/reference/reorg_seurat_files.html

docs/reference/reset_seu_meta.html

docs/reference/run_BEAM.html

docs/reference/run_census.html

docs/reference/run_enrichmentbrowser.html

docs/reference/run_hmap.html

docs/reference/run_scvelo.html

docs/reference/run_seurat_de.html

docs/reference/save_seurat.html

docs/reference/sce_from_tibbles.html

docs/reference/set_colnames_txi.html

docs/reference/seu_calcn.html

docs/reference/seu_complex_heatmap.html

docs/reference/seu_from_tibbles.html

docs/reference/seu_from_tximport.html

docs/reference/seuratApp.html

docs/reference/seurat_cluster.html

docs/reference/seurat_find_markers.html

docs/reference/seurat_integrate.html

docs/reference/seurat_integration_pipeline.html

docs/reference/seurat_pipeline.html

docs/reference/seurat_preprocess.html

docs/reference/seurat_reduce_dimensions.html

docs/reference/stash_marker_features.html

docs/reference/subset_by_meta.html

docs/reference/swap_counts_from_feature.html

docs/reference/tableSelected.html

docs/reference/tableSelectedui.html

docs/reference/techInfo.html

docs/reference/techInfoui.html

docs/reference/threshold_monocle_genes.html

docs/reference/transcripts_to_genes.html

docs/reference/unite_metadata.html

docs/reference/update_chevreul_object.html

docs/reference/update_exp_meta.html

docs/reference/update_human_gene_symbols.html

docs/reference/update_project_db.html

docs/reference/update_seu_meta.html

docs/search.json

docs/sitemap.xml

inst/extdata/clustree.png

inst/extdata/louvain_and_feature_umap_plot.png

inst/extdata/monocle_final_steps.png

inst/extdata/monocle_first_steps.png

inst/extdata/multiple_feature_density_umap.png

inst/extdata/pair_of_histograms.png

inst/extdata/seuratTools_integration.png

inst/extdata/velocity_in_seuratTools.png

inst/helpers/allTranscripts.md inst/helpers/clustree.md inst/helpers/comparePlots.md inst/helpers/diffex.md inst/helpers/findMarkers.md inst/helpers/heatMap.md inst/helpers/integrateProjects.md inst/helpers/monocle.md inst/helpers/overview.md inst/helpers/pathwayEnrichment.md inst/helpers/plotVelocity.md inst/helpers/preprocessing.md inst/helpers/reformatMetadata.md inst/helpers/regressFeatures.md inst/helpers/subsetSeurat.md inst/helpers/violinPlot.md man/Monocle2_diffex.Rd man/SetDefaultAssay.Rd man/add_census_slot.Rd man/add_percent_mito.Rd man/add_read_count_col.Rd man/allTranscripts.Rd man/allTranscriptsui.Rd man/annotate_cell_cycle.Rd man/annotate_excluded.Rd man/append_to_project_db.Rd man/arrange_ptime_heatmaps.Rd man/assign_clusters_to_cds.Rd man/build_bigwig_db.Rd man/by_row_corr_between_pt_heatmaps.Rd man/calc_cor_across_heatmaps.Rd man/calc_pseudotime_heatmap.Rd man/ccScore.Rd man/ccScoreui.Rd man/cells_selected.Rd man/celltype_markers.Rd man/changeEmbedParams.Rd man/changeEmbedParamsui.Rd man/clustering_workflow.Rd man/combine_cols.Rd man/combine_looms.Rd man/convert_human_seu_to_mouse.Rd man/convert_monoclev2_to_seuv3.Rd man/convert_mouse_seu_to_human.Rd man/convert_seu_list_to_multimodal.Rd man/convert_seu_to_cds.Rd man/convert_seurat_to_sce.Rd man/convert_seuv3_to_monoclev2.Rd man/convert_symbols_by_species.Rd man/convert_v3_to_v5.Rd man/create_proj_matrix.Rd man/create_project_db.Rd man/cross_check_heatmaps.Rd man/cross_species_integrate.Rd man/default_helper.Rd man/diffex.Rd man/diffexui.Rd man/dockerSeuratApp.Rd man/dot-send_enrichr_query.Rd man/dropdownButton.Rd man/enframe_markers.Rd man/filter_low_rc_cells.Rd man/filter_merged_seu.Rd man/filter_merged_seus.Rd man/filter_rows_to_top.Rd man/findMarkers.Rd man/findMarkersui.Rd man/find_all_markers.Rd man/flip_pseudotime.Rd man/format_new_metadata.Rd man/format_pathway_table.Rd man/gene_test_plot.Rd man/genes_to_transcripts.Rd man/getEnrichedPathways.Rd man/get_meta.Rd man/get_transcripts_from_seu.Rd man/global_cellalign.Rd man/harmony_integrate.Rd man/human_to_mouse_homologs.Rd man/integrateProj.Rd man/integrateProjui.Rd man/integration_workflow.Rd man/label_transfer.Rd man/learn_graph_by_resolution.Rd man/list_plot_types.Rd man/load_bigwigs.Rd man/load_counts_by_tximport.Rd man/load_meta.Rd man/load_seurat_from_proj.Rd man/load_seurat_path.Rd man/local_cellalign.Rd man/make_bigwig_db.Rd man/make_seuratTools_clean_names.Rd man/mem_str.Rd man/merge_loom.Rd man/merge_small_seus.Rd man/metadata_from_batch.Rd man/minimalSeuratApp.Rd man/monocle.Rd man/monocle_module_heatmap.Rd man/monocleui.Rd man/nil.Rd man/pad_sample_files.Rd man/pathwayEnrichment.Rd man/pathwayEnrichmentui.Rd man/pipe.Rd man/plotClustree.Rd man/plotClustree_UI.Rd man/plotCoverage.Rd man/plotCoverage_UI.Rd man/plotDimRed.Rd man/plotDimRedui.Rd man/plotHeatmap.Rd man/plotHeatmapui.Rd man/plotReadCount.Rd man/plotReadCountui.Rd man/plotViolin.Rd man/plotViolinui.Rd man/plot_all_ptimes.Rd man/plot_all_transcripts.Rd man/plot_cds.Rd man/plot_cell_cycle_distribution.Rd man/plot_cells.Rd man/plot_feature.Rd man/plot_feature_in_ref_query_ptime.Rd man/plot_gene_coverage_by_var.Rd man/plot_markers.Rd man/plot_monocle_features.Rd man/plot_multiple_branches_heatmap.Rd man/plot_pseudotime.Rd man/plot_pseudotime_heatmap.Rd man/plot_readcount.Rd man/plot_scvelo.Rd man/plot_transcript_composition.Rd man/plot_var.Rd man/plot_violin.Rd man/plotly_settings.Rd man/prep_armor_meta.Rd man/prep_plot_genes_in_pseudotime.Rd man/prep_slider_values.Rd man/process_monocle_child.Rd man/propagate_spreadsheet_changes.Rd man/query_experiment.Rd man/read_project_db.Rd man/record_experiment_data.Rd man/reference_integrate.Rd man/reformatMetadataDR.Rd man/reformatMetadataDRui.Rd man/regress_by_features.Rd man/reintegrate_seu.Rd man/rename_from_x_notation.Rd man/rename_seurat.Rd man/reorg_seurat_files.Rd man/reset_seu_meta.Rd man/run_BEAM.Rd man/run_census.Rd man/run_enrichmentbrowser.Rd man/run_hmap.Rd man/run_seurat_de.Rd man/save_seurat.Rd man/sce_from_tibbles.Rd man/scvelo_expression.Rd man/set_colnames_txi.Rd man/seu_calcn.Rd man/seu_complex_heatmap.Rd man/seu_from_tibbles.Rd man/seu_from_tximport.Rd man/seuratApp.Rd man/seuratTools-package.Rd man/seuratToolsBox.Rd man/seurat_cluster.Rd man/seurat_find_markers.Rd man/seurat_integrate.Rd man/seurat_integration_pipeline.Rd man/seurat_pipeline.Rd man/seurat_preprocess.Rd man/seurat_reduce_dimensions.Rd man/seurat_v5_integrate.Rd man/seurat_v5_integration_pipeline.Rd man/stash_marker_features.Rd man/subset_by_meta.Rd man/swap_counts_from_feature.Rd man/tableSelected.Rd man/tableSelectedui.Rd man/techInfo.Rd man/techInfoui.Rd man/threshold_monocle_genes.Rd man/transcripts_to_genes.Rd man/unite_metadata.Rd man/update_exp_meta.Rd man/update_human_gene_symbols.Rd man/update_project_db.Rd man/update_seu_meta.Rd man/update_seuratTools_object.Rd man/velocyto_assay.Rd man/velocyto_seu.Rd man/velocyto_seurat_from_loom.Rd

rsconnect/shinyapps.io/kevin-stachelek/seuratTools.dcf

tests/testthat.R tests/testthat/test-clustering_workflow.R tests/testthat/test-cross_species.R tests/testthat/test-misc.R tests/testthat/test-monocle_module_heatmap.R tests/testthat/test-pipeline.R tests/testthat/test-seurat_annotation.R tests/testthat/test-seurat_cluster.R tests/testthat/test-seurat_integrate.R tests/testthat/test-seurat_pipeline.R tests/testthat/test-seurat_preprocess.R tests/testthat/test-workflow.R

vignettes/.gitignore

vignettes/articles/images/GoToWebinar_002.png

vignettes/articles/images/Heatmap.png

vignettes/articles/images/Heatmap2.0.png

vignettes/articles/images/PlotCoverage.png

vignettes/articles/images/PlotCoverage2.0.png

vignettes/articles/images/Screenshot_2023-08-25_at_1.28.26_PM.png

vignettes/articles/images/Screenshot_2023-08-25_at_1.40.35_PM.png

vignettes/articles/images/Screenshot_2023-08-25_at_1.40.57_PM.png

vignettes/articles/images/clustree.png

vignettes/articles/images/integration_image.png

vignettes/articles/images/louvain_and_feature_umap_plot.png

vignettes/articles/images/marker_gene_plot.png

vignettes/articles/images/monocle_final_steps.png

vignettes/articles/images/monocle_first_steps.png

vignettes/articles/images/pair_of_histograms.png

vignettes/articles/images/transcript_composisiont.png

vignettes/articles/images/unnamed-chunk-9-1.png

vignettes/articles/images/violinPlot.png

vignettes/articles/integration.Rmd vignettes/articles/pipeline.Rmd vignettes/articles/preprocessing.Rmd

vignettes/articles/preprocessing_files/figure-html/unnamed-chunk-13-1.png

vignettes/articles/preprocessing_files/figure-html/unnamed-chunk-14-1.png

vignettes/articles/preprocessing_files/figure-html/unnamed-chunk-2-1.png

vignettes/articles/shiny_app.Rmd vignettes/articles/visualization.Rmd

whtns/seuratTools documentation built on May 14, 2024, 2:29 p.m.