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
