Files in maehrlab/thymusatlastools
Tools for analysis of single-cell transcriptomic data

.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/classifier.R R/classifier.Rmd R/data_handling.R R/data_handling.Rmd R/exploratory_pipeline.R R/exploratory_pipeline.Rmd R/plotting.R R/plotting.Rmd R/pseudotime.R R/pseudotime.Rmd R/pseudotime_plotting.R R/pseudotime_plotting.Rmd R/quality_control.R R/quality_control.Rmd R/setup.R R/setup.Rmd R/seurat_extra.R R/seurat_extra.Rmd R/utilities.R R/utilities.Rmd README.md
data/ALL_TCR_GENES.rda
data/Y_genes.rda
data/cc_genes.rda
data/handpicked_markers.rda
data/mouse_tfs.rda
data/orthologs_ens87.rda
data/poised_genes.rda
data/ramilowski.rda
man/.Rapp.history
man/AvailableData.Rd man/ClusterBag.Rd man/ClusterBagStability.Rd man/DESummaryFast.Rd man/ExploreIteratively.Rd man/FetchDataZeroPad.Rd man/FillNA.Rd man/FindMarkersFlex.Rd man/KMeansGapStat.Rd man/ProjectCells.Rd man/RefineVariableGenes.Rd man/SanitizeGenes.Rd man/SeuratMerge.Rd man/SeuratPie.Rd man/SubsetDataFlex.Rd man/TACS.Rd man/add_cc_score.Rd man/add_maehrlab_metadata.Rd man/add_pseudotime_to_seurat.Rd man/add_quadrants.Rd man/add_rp_mt_percentage.Rd man/add_rp_percentage.Rd man/add_tcr.Rd man/aggregate_nice.Rd man/align_embedding_to_reference.Rd man/annot_ident_plot.Rd man/are_compatible.Rd man/call_monocle_on_seurat.Rd man/check_xist_all.Rd man/check_xist_pure.Rd man/classify_mlr.Rd man/cluster_wrapper.Rd man/collapse_by_name.Rd man/convert_species_dge.Rd man/custom.make.unique.Rd man/custom_feature_plot.Rd man/dendrogram_merge_points.Rd man/deseuratify_raw_data.Rd man/dge_merge_list.Rd man/dir.create.nice.Rd man/do_enrichr.Rd man/expected_doublet_counts.Rd man/explore_embeddings.Rd man/export_from_seurat.Rd man/facet_plot_gene_clusters.Rd man/faceted_tsne.Rd man/fix_cluster_order.Rd man/get_cTEC_mTEC_genes.Rd man/get_classifier_coefs.Rd man/get_macosko_cc_genes.Rd man/get_metadata.Rd man/get_mouse_tfs.Rd man/get_ortholog.Rd man/get_ortholog_nonvec.Rd man/get_ortholog_table.Rd man/get_poised_genes.Rd man/get_preimage.Rd man/get_ramilowski.Rd man/get_rene_markers.Rd man/get_similar_genes.Rd man/harmonize_species.Rd man/has_ortholog.Rd man/heatmap_gene_clusters.Rd man/is_mt.Rd man/is_rp.Rd man/knn_classifier.Rd man/load_thymus_profiling_data.Rd man/make_heatmap_for_table.Rd man/master_pt.Rd man/misc_summary_info.Rd man/normalize_cpx_amt.Rd man/outlier_labeled_scatterplot.Rd man/pc_as_pt.Rd man/plot_dendro_with_rect.Rd man/remove_TEC_doublets.Rd man/remove_species_specific_genes.Rd man/replace_with_int_rank.Rd man/save_depth_stats.Rd man/save_feature_plots.Rd man/save_marker_table.Rd man/seuratify_thy_data.Rd man/smooth_and_cluster_genes.Rd man/strip_suffix.Rd man/strsplit_drop.Rd man/text2file.Rd man/time_series.Rd man/time_series_save.Rd man/train_save_classifier.Rd man/tsne_colored.Rd man/wheel_plot.Rd
tables/Absolute cell numbers.csv
tables/CellCycleGenes.txt
tables/GOterm_ms_cellcycle.txt
tables/Lesch2016_NatGen_PoisedGenes.txt
tables/LigandReceptor_Ramilowski2015.txt
tables/LigandReceptor_Ramilowski2015.xlsx
tables/LigandReceptor_Ramilowski2015_mouse.txt
tables/Macosko_cell_cycle_genes.txt
tables/cTEC_mTEC_data_driven.txt
tables/cell_type_markers.csv
tables/cell_type_markers_long.csv
tables/cellcycle.txt
tables/chrY_genes.txt
tables/genes_to_display_Figure4b.txt
tables/genes_to_display_Figure5b.txt
tables/genes_to_display_Figure6d.txt
tables/ligand_name_conversion.txt
tables/mCellAdhesion_pantherPC00069.txt
tables/mCellJunction_pantherPC00070.txt
tables/mExtracellMatrix_pantherPC00102.txt
tables/mHydrolases_pantherPC00121.txt
tables/mImmunity_pantherPC00090.txt
tables/mNucleicBinding_pantherPC00171.txt
tables/mProtease_pantherPC00190.txt
tables/mReceptor_pantherPC00197.txt
tables/mSignalingMol_pantherPC00207.txt
tables/mTranscriptionFactor_pantherPC00218.txt
tables/metadata.txt
tables/mouse_genes_ensembl.txt
tables/mouse_tfs.txt
tables/mousegene_matchedHumanOrth.txt
tables/mousegene_matchedHumanOrth_OLD.csv
tables/ms_cellcycleGO0007049.txt
tables/mscellcycle.txt
tables/mscellcycle_new.txt
tables/pathways_joost2016.txt
tables/senescence.txt
tables/top markers initial report.zip
tables/uniprot-keyword%3A-Receptor+%5BKW-0675%5D-+AND+reviewed%3Ayes+AND+organism%3--.tab
maehrlab/thymusatlastools documentation built on June 1, 2018, 10:09 a.m.