API for AllenInstitute/scrattch.hicat
Hierarchical Iterative Clustering Analysis for Transcriptomic data

Global functions
CCA Source code
DE_genes_cat_by_cl Source code
DE_genes_pairs Source code
DE_genes_pw Source code
build_dend Source code
calc_tau Man page Source code Source code
cl_max_tau Source code
collect_co_matrix Man page Source code
collect_co_matrix_sparseM Man page Source code
collect_subsample_cl_matrix Source code
compare_annotate Man page Source code
convert_pair_matrix Man page Source code
cpm Man page Source code
cutree_dend Source code
de_pair Source code
de_param Man page Source code
de_score Man page Source code
de_score_pairs Source code
dend_lca Source code
dend_list Source code
display_cl Source code
display_cl_markers_co.ratio Source code
fast_tsne Source code
filter_gene_mod Source code
findDendMarkers Source code
findDendMarkersSpecficity Source code
findNodeSpecificMarkers Source code
findVG Source code
find_doublet Source code
getGroupSpecificMarkers Source code
getNodeSpecificMarkers Source code
getNodeVsSiblingMarkers Source code
get_cell.cl.co.ratio Man page Source code
get_cl_co_stats Source code
get_cl_mat Man page Source code
get_cl_means Man page Source code
get_cl_medians Man page Source code
get_cl_sums Man page Source code
get_color Source code
get_cols Source code
get_core_transition Source code
get_de_genes_sym Source code
get_de_score Source code
get_dend_markers Source code
get_dend_parent Source code
get_eigen Man page Source code
get_gene_score Source code
get_pair_matrix Man page Source code
get_pair_matrix_coor Man page Source code
group_specific_markers Source code
heatmap.3 Source code
init_cut Source code
iter_clust Man page Source code
iter_consensus_clust Man page Source code
jaccard Man page Source code
jaccard_louvain Man page Source code
jaccard_louvain.FNN Man page Source code
label_dend Source code
lm_matrix Source code
lm_normalize Source code
logCPM Source code
mapDendMarkers Source code
map_by_cor Man page Source code
map_cl_summary Man page Source code
map_cv Source code
map_sampling Man page Source code
markers_max_tau Source code
markers_tau_one_vs_other Source code
merge_cl Man page Source code
merge_cl_by_co Source code
merge_co_matrix Source code
multiplot Source code
node_specific_markers Source code
node_vs_sibling_markers Source code
onestep_clust Man page Source code
pass_louvain Source code
plot_cell_cl_co_matrix Source code
plot_cl_heatmap Source code
plot_cl_meta_barplot Source code
plot_co_matrix Source code
plot_de_lfc_num Source code
plot_de_num Source code
plot_dend Source code
plot_river Source code
plot_tsne_cl Source code
plot_tsne_gene Source code
plot_tsne_meta Source code
predict_annotate_cor Source code
prune_dend Source code
pvclust_show_signif_gradient Source code
rd_PCA Source code
rd_WGCNA Source code
refine_cl Source code
reorder_cl Man page Source code
reorder_dend Source code
run_consensus_clust Man page Source code
sample_cells Man page Source code
sample_cells_by_genecounts Man page
sample_cl_list Source code
score_gene_mod Source code
selectMarkersPair Source code
selectMarkersPairDirection Source code
selectMarkersPairGroup Source code
selectNMarkers Source code
select_N_markers Source code
select_markers Source code
select_markers_pair Source code
select_markers_pair_direction Source code
set_pair_matrix Man page Source code
sparse_cor Man page Source code
tau_one_vs_other_genes Source code
test_cv_cor Source code
unbranch_by_conf Source code
unbranch_by_length Source code
update_hicat Source code
vec_chisq_test Source code
within_group_specific_markers Source code
AllenInstitute/scrattch.hicat documentation built on Feb. 26, 2019, 6:38 p.m.