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

Global functions
AvailableData Man page Source code
Capitalize Source code
ClusterBag Man page Source code
ClusterBagStability Man page Source code
DESummaryFast Man page Source code
ExploreIteratively Man page Source code
FetchDataZeroPad Man page Source code
FillNA Man page Source code
FindMarkersFlex Man page Source code
KMeansGapStat Man page Source code
ProjectCells Man page Source code
RefineVariableGenes Man page Source code
SanitizeGenes Man page Source code
SeuratMerge Man page Source code
SeuratPie Man page Source code
SubsetDataFlex Man page Source code
TACS Man page Source code
add_cc_score Man page Source code
add_maehrlab_metadata Man page Source code
add_pseudotime_to_seurat Man page Source code
add_quadrants Man page Source code
add_rp_mt_percentage Man page Source code
add_rp_percentage Man page Source code
add_tcr Man page Source code
aggregate_nice Man page Source code
align_embedding_to_reference Man page Source code
annot_ident_plot Man page Source code
are_compatible Man page Source code
atae Source code
atat Source code
call_monocle_on_seurat Man page Source code
check_xist_all Man page Source code
check_xist_pure Man page Source code
classify_mlr Man page Source code
cluster_summary Source code
cluster_wrapper Man page Source code
collapse_by_name Man page Source code
compare_views Source code
convert_species_dge Man page Source code
custom.make.unique Man page Source code
custom_feature_plot Man page Source code
dendrogram_merge_points Man page Source code
deseuratify_raw_data Man page Source code
dge_merge_list Man page Source code
dir.create.nice Man page Source code
distance_sq Source code
div_by_max Source code
div_by_sum Source code
do_dim_red Source code
do_enrichr Man page Source code
down_idx Source code
expected_doublet_counts Man page Source code
explore_embeddings Man page Source code
export_from_seurat Man page Source code
facet_plot_gene_clusters Man page Source code
faceted_tsne Man page Source code
factor_numeric Source code
fix_cluster_order Man page Source code
flip_table Source code
get_cTEC_mTEC_genes Man page Source code
get_classifier_coefs Man page Source code
get_macosko_cc_genes Man page Source code Source code
get_metadata Man page Source code
get_mouse_tfs Man page Source code Source code
get_ortholog Man page Source code
get_ortholog_nonvec Man page Source code
get_ortholog_table Man page Source code Source code
get_poised_genes Man page Source code Source code
get_preimage Man page Source code
get_ramilowski Man page Source code Source code
get_rene_markers Man page Source code Source code
get_similar_genes Man page Source code
harmonize_species Man page Source code
has_ortholog Man page Source code
heatmap_gene_clusters Man page Source code
is_mt Man page Source code
is_rp Man page Source code
knn_classifier Man page Source code
load_thymus_profiling_data Man page Source code
make_heatmap_for_table Man page Source code
master_pt Man page Source code
matrixify_preserving_rownames Source code
misc_summary_info Man page Source code
multiplot Source code
na2zero Source code
nnz Source code
normalize_cpx_amt Man page Source code
onLoad Source code
outlier_labeled_scatterplot Man page Source code
pc_as_pt Man page Source code
percentify Source code
plot_dendro_with_rect Man page Source code
prop_nz Source code
remove_TEC_doublets Man page Source code
remove_species_specific_genes Man page Source code
replace_with_int_rank Man page Source code
save_complexity_plot Source code
save_depth_stats Man page Source code
save_feature_plots Man page Source code
save_marker_table Man page Source code
save_plot_grid Source code
screen_receptor_ligand Source code
seuratify_thy_data Man page Source code
smooth_and_cluster_genes Man page Source code
standardize Source code
strip_suffix Man page Source code
strsplit_drop Man page Source code
text2file Man page Source code
time_series Man page Source code
time_series_save Man page Source code
top_genes_by_pc Source code
top_n_preserve_rownames Source code
train_save_classifier Man page Source code
tsne_colored Man page Source code
var_gene_select Source code
vectorize_preserving_rownames Source code
wheel_plot Man page Source code
maehrlab/thymusatlastools documentation built on June 1, 2018, 10:09 a.m.