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

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

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

Global functions
CCA Man page Source code
CanonCor Man page Source code
DE_genes_cat_by_cl Man page Source code
DE_genes_pairs Man page Source code
DE_genes_pw Man page Source code
adjust_color Man page Source code
angle Man page Source code
avgangle Man page Source code
batch_process Man page Source code
build_dend Man page Source code
build_dend_harmonize Man page Source code
build_dend_with_means Man page Source code
build_tsne Man page Source code
calc_tau Man page Source code
check_donor Man page Source code
check_neun Man page Source code
check_outlier Man page Source code
check_qc Man page Source code
clean_outliers Man page Source code
collect_co_matrix Man page Source code
collect_subsample_cl_matrix Source code
comb_de_result Man page Source code
combine_cl Man page Source code Source code
combine_finer_split Source code
compare_annotate Man page Source code
compare_plot Man page Source code
compile_cl_mat Source code
compute_knn Man page Source code
compute_vg_stats Man page Source code
convert_pair_matrix Man page Source code
convert_pair_matrix_str Man page Source code
cpm Man page Source code
create_pairs Man page Source code
cutree_dend Man page Source code
de_all_pairs Man page Source code
de_genes_pairs_multiple Man page Source code
de_pair Man page Source code
de_pair_chisq Man page Source code
de_pair_limma Man page Source code
de_param Man page Source code
de_score Man page Source code
de_score_pairs Man page Source code
de_selected_pairs Man page Source code
de_stats_all_pairs Man page Source code
de_stats_pair Man page Source code
de_stats_selected_pairs Man page Source code
dend_lca Man page Source code
dend_list Man page Source code
dend_match Man page Source code
display_cl Man page Source code
display_cl4 Man page Source code
display_cl_markers_co.ratio Man page Source code
display_cl_one_vs_others Man page Source code
doubletFinder Man page Source code
edgeMaker Man page Source code
fast_tsne Man page Source code
filter_RD Source code
filter_by_size Source code
filter_gene_mod Source code
findVG Man page Source code
find_doublet Man page Source code
find_doublet_all Source code
find_low_quality_all Source code
find_low_quality_cl Man page Source code
find_vg Man page Source code
gene_dispersion Man page Source code
gene_gene_cor_conservation Man page Source code
gene_loess_fit Man page Source code
gene_loess_fit_z Man page Source code
gene_means Man page Source code
gene_vars Man page Source code
gene_z Man page Source code
get.markers.num Man page Source code
getTopMarkersByPropNew Man page Source code
get_RD_cl_center Man page Source code
get_beta_score Man page Source code
get_cell.cl.co.ratio Man page Source code
get_cl_df Man page Source code
get_cl_mat Man page Source code
get_cl_means Man page Source code
get_cl_means_list Man page Source code
get_cl_medians Man page Source code
get_cl_present_list Man page Source code
get_cl_prop Man page Source code
get_cl_sim Man page Source code
get_cl_sim_multiple Man page Source code
get_cl_sums Man page Source code
get_co_ratio Source code
get_core_intermediate Man page Source code
get_de_genes_sym Man page Source code
get_de_lfc_list Man page Source code
get_de_matrix Man page Source code
get_de_pair Man page Source code
get_de_result Man page Source code
get_de_score Man page Source code
get_dend_markers Man page Source code
get_dend_markers_direction Man page Source code
get_dend_parent Man page Source code
get_eigen Man page Source code
get_gene_cl_correlation Man page Source code Source code
get_gene_score Man page Source code
get_knn Man page Source code
get_knn_batch Man page Source code
get_knn_graph Man page Source code
get_knn_weight Man page Source code
get_pair_matrix Man page Source code
get_pair_matrix_coor Man page Source code
get_pairs Man page Source code
group_cl Man page Source code
group_specific_markers Man page Source code
harmonize Man page Source code
heatmap.3 Man page
heatmap.4 Man page
i_harmonize Man page Source code
impute_knn Man page Source code
impute_knn_global Man page Source code
impute_val_cor Man page Source code Source code
incrementHex Man page Source code
init_cut Source code
iter_clust Man page Source code
iter_consensus_clust Man page Source code
iter_impute_knn Man page Source code
jaccard Man page Source code
jaccard_leiden Man page Source code
jaccard_leiden.RANN Man page Source code
jaccard_louvain Man page Source code
jaccard_louvain.RANN Man page Source code
knn_cor Man page Source code
knn_cosine Man page Source code
knn_jaccard Source code
knn_jaccard_louvain Man page Source code
knn_joint Man page Source code
label_dend Man page Source code
lm_matrix Man page Source code
lm_normalize Man page Source code
logCPM Man page Source code
makeColorsUnique Man page Source code
makeLayerLabel Man page Source code
makeRegionLabel Man page Source code
map_by_cor Man page Source code
map_cl_summary Man page Source code
map_cv Man page Source code
map_dend Man page Source code
map_dend_markers Man page Source code
map_dend_membership Man page Source code
map_sampling Man page Source code
mapping Man page Source code
markers_max_tau Man page Source code
markers_tau_one_vs_other Man page Source code
match_cl Man page Source code
merge_cl Man page Source code
merge_cl_by_co Source code
merge_cl_multiple Man page Source code
merge_knn_result Man page Source code
multiplot Man page Source code
mybgplot3d Man page Source code
node_specific_markers Man page Source code
node_vs_sibling_markers Man page Source code
onestep_clust Man page Source code
pair_cor Man page Source code
pass_louvain Source code
perp Man page Source code
perpEnd Man page Source code
perpMid Man page Source code
perpStart Man page Source code
plot_2d_select Man page Source code
plot_3d_label Man page Source code
plot_3d_label_multiple Man page Source code
plot_3d_select Man page Source code
plot_3d_val Man page Source code
plot_RD_cl Man page Source code
plot_RD_gene Man page Source code
plot_RD_meta Man page Source code
plot_cell_cl_co_matrix Source code
plot_cl_cells Man page Source code
plot_cl_heatmap Man page Source code
plot_cl_heatmap4 Man page Source code
plot_cl_low Man page Source code
plot_cl_meta_barplot Man page Source code
plot_co_matrix Source code
plot_confusion Man page Source code
plot_constellation Source code
plot_de_lfc_num Man page Source code
plot_de_num Man page Source code
plot_dend Man page Source code
plot_doublet Man page Source code
plot_low_qc Man page Source code
plot_markers Man page Source code
plot_markers_cl_means Man page Source code
plot_pair_matrix Man page Source code
plot_tSNE_gene Man page Source code
plot_tSNE_meta Man page Source code
plot_tsne Man page Source code Source code
plot_tsne_cl Man page Source code
plot_vg Man page Source code
prcomp.irlba Man page Source code
predict_annotate_cor Man page Source code
predict_knn Man page Source code
predict_knn_new Man page Source code
prepare_harmonize Source code
prune_dend Man page Source code
pvclust_show_signif_gradient Man page
rd_PCA Man page Source code
rd_Umap Man page Source code
rd_WGCNA Source code
refine_cl Man page Source code
renameAndOrderClusters Man page Source code
reorder_cl Man page Source code
reorder_dend Man page Source code
reorder_factor Man page Source code
rescale_samples Man page Source code
resolve_cl Man page Source code
run_consensus_clust Man page Source code
sample_cells Man page Source code
sample_cl_list Source code
sample_sets_list Man page Source code
score_gene_mod Source code
select_N_markers Man page Source code
select_dend_markers Man page Source code
select_joint_genes Man page Source code
select_joint_markers Man page Source code
select_markers Man page Source code
select_markers_pair Man page Source code
select_markers_pair_direction Man page Source code
select_markers_pair_group Man page Source code
select_node_specific_markers Man page Source code
select_pos_dend_markers Man page Source code
select_pos_markers Man page Source code
set_pair_matrix Man page Source code
sim_knn Man page Source code
simple_dend Man page Source code
sparse_cor Man page Source code
summarize_cl Man page Source code
test_knn Man page Source code
test_merge Man page Source code
unbranch_by_conf Man page Source code
unbranch_by_length Man page Source code
updateSampDat Man page Source code
vec_chisq_test Man page Source code
within_group_specific_markers Man page Source code
AllenInstitute/scrattch.hicat documentation built on Oct. 20, 2023, 6:55 a.m.

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