AllenInstitute/scrattch.bigcat
Iterative Clustering Analysis for Transcriptomic data for big matrix

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377
Source code
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AllenInstitute/scrattch.bigcat: Iterative Clustering Analysis for Transcriptomic data for big matrix
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API for AllenInstitute/scrattch.bigcat
Iterative Clustering Analysis for Transcriptomic data for big matrix

Global functions
ComputeSNN Source code
DirectSNNToFile Source code
FastCov Source code
FastCovMats Source code
FastLogVMR Source code
FastRBind Source code
FastSparseRowScale Source code
FastSparseRowScaleWithKnownStats Source code
GraphToNeighborHelper Source code
ImputeKnn Source code
LogNorm Source code
PCA_umap Source code
ReplaceColsC Source code
RowMergeMatrices Source code
RowMergeMatricesList Source code
RowVar Source code
SparseRowMean Source code
SparseRowVar Source code
SparseRowVar2 Source code
SparseRowVarStd Source code
Standardize Source code
WriteEdgeFile Source code
adjust_color Source code
angle Source code
append_big.dat_fbm Source code
append_big.dat_parquet Source code
avgangle Source code
batch_process Source code
big.dat.parquet.to.h5 Source code
big.dat_logNormal_parquet Source code
big.dat_subset_fbm Source code
big_dat_apply Source code
big_project Source code
build_annoy_index Source code
build_dend Source code
build_train_index Source code Source code
build_train_index_bs Source code
build_tsne Source code
calc_tau Source code
cbind_big.dat_fbm Source code
cell_cl_cor Source code
check_pairs_ds Source code
check_pairs_lfc Source code
check_triplet Source code
check_triplet_big Source code
cleanAnnoyIndex Source code
clean_group_color Source code
clean_group_id Source code
clean_outliers Source code
collect_co_matrix Source code
collect_subsample_cl_matrix Source code
comb_de_result_big Source code
combine_cl Source code
combine_cl_sim Source code
combine_finer_split Source code
compare_annotate Source code
compile_cl_mat Source code
compute_knn Source code
compute_vg_stats Source code
convert_big.dat_fbm Source code
convert_big.dat_parquet Source code
convert_mat_list_big.dat_fbm Source code
convert_mat_list_big.dat_parquet Source code
convert_pair_matrix Source code
convert_pair_matrix_str Source code
cpm Source code
create_big.dat_fbm Source code
create_pairs Source code
cutree_dend Source code
de_all_pairs Source code
de_genes_multiple Source code
de_genes_pairs_multiple Source code
de_pair_chisq Source code
de_pair_fast_limma Source code
de_pair_limma Source code
de_pair_summary Source code
de_pair_t.test Source code
de_param Source code
de_selected_pairs Source code
de_stats_pair Source code
dend_lca Source code
dend_list Source code
dend_match Source code
display_cl Source code
display_cl4 Source code
display_cl_big Source code
display_cl_markers_co.ratio Source code
display_cl_one_vs_others Source code
edgeMaker Source code
export_de_genes Source code
fast_tsne Source code
fbm_to_parquet Source code
filter_RD Source code
filter_by_size Source code
filter_cols Source code
filter_gene_mod Source code
findElbowPoint Source code
find_doublet Source code
find_doublet_all Source code
find_doublet_by_marker Source code
find_doublets_all_big Source code
find_low_quality Source code
find_low_quality_big Source code
find_triplets_big Source code
find_vg Source code
gene_dispersion Source code
gene_gene_cor_conservation Source code
gene_loess_fit Source code
gene_loess_fit_z Source code
gene_means Source code
gene_vars Source code
gene_z Source code
get_PCA Source code
get_RD_cl_center Source code
get_beta_score Source code
get_big_bins Source code
get_cell.cl.co.ratio Source code
get_cl_df Source code
get_cl_mat Source code
get_cl_means Source code
get_cl_means_R Source code
get_cl_medians Source code
get_cl_medians_R Source code
get_cl_present Source code
get_cl_prop Source code
get_cl_sigma Source code
get_cl_sim Source code
get_cl_sim_multiple Source code
get_cl_sqr_means Source code
get_cl_stats Source code
get_cl_stats_big Source code
get_cl_stats_fbm Source code
get_cl_stats_list Source code
get_cl_stats_parquet Source code
get_cl_sums Source code
get_cl_sums_R Source code
get_cl_vars Source code
get_co_ratio Source code
get_cols Source code
get_cols_delayedArray Source code
get_cols_fbm Source code
get_cols_parquet Source code
get_cols_parquet_dense Source code
get_counts Source code
get_de_genes Source code
get_de_genes_sym Source code
get_de_matrix Source code
get_de_pair Source code
get_de_pair_big Source code
get_de_result_big Source code
get_de_result_recursive Source code
get_de_score Source code
get_de_truncate_score_sum Source code
get_dend_markers Source code
get_dend_markers_direction Source code
get_dend_parent Source code
get_eigen Source code
get_gene_cl_correlation Source code
get_gene_score Source code
get_gene_score_ds Source code
get_genes_mat Source code
get_impute_knn Source code Source code
get_knn Source code
get_knn_batch Source code
get_knn_batch_big Source code
get_knn_graph Source code
get_knn_pairs Source code
get_knn_weight Source code
get_logNormal Source code
get_pair_matrix Source code
get_pair_matrix_coor Source code
get_pairs Source code
get_row_means Source code
get_row_sums Source code
get_row_vars Source code
get_weighted_means Source code
group_specific_markers Source code
harmonize Source code
i_harmonize Source code
impute_cross_big Source code
impute_dat_big Source code
impute_knn Source code
impute_knn_cross Source code
impute_knn_global Source code Source code
impute_knn_global_big Source code Source code
init_big.dat_parquet Source code
init_cut Source code
init_mat_parqeut_dense Source code
iter_clust Source code
iter_clust_big Source code
iter_clust_merge Source code
iter_clust_merge_big Source code
iter_consensus_clust Source code
jaccard Source code
jaccard_big Source code
jaccard_leiden Source code
jaccard_louvain Source code
jaccard_louvain.RANN Source code
knn_combine Source code Source code
knn_jaccard Source code
knn_jaccard_clust Source code
knn_joint Source code
l2norm Source code
label_dend Source code
lm_matrix Source code
lm_normalize Source code
logCPM Source code
map_by_cor Source code
map_cells_knn Source code
map_cells_knn_big Source code
map_cells_knn_bs Source code
map_cl_summary Source code
map_cv Source code
map_sampling Source code
markers_max_tau Source code
markers_tau_one_vs_other Source code
match_cl Source code
merge_cl Source code
merge_cl_big Source code
merge_cl_by_co Source code
merge_cl_multiple Source code
multiplot Source code
mybgplot3d Source code
null_de Source code
onestep_clust Source code
onestep_clust_big Source code
pair_cor Source code
pass_louvain Source code
perp Source code
perpEnd Source code
perpMid Source code
perpStart Source code
plot_2d_select Source code
plot_2d_umap_anno Source code
plot_3d_label Source code
plot_3d_label_multiple Source code
plot_3d_select Source code
plot_3d_umap_anno Source code
plot_3d_val Source code
plot_RD_cl Source code
plot_RD_cl_subset Source code
plot_RD_gene Source code
plot_RD_highlight Source code
plot_RD_meta Source code
plot_cell_cl_co_matrix Source code
plot_cl_cells Source code
plot_cl_heatmap Source code
plot_cl_heatmap4 Source code
plot_cl_meta_barplot Source code
plot_co_matrix Source code
plot_confusion Source code
plot_de_lfc_num Source code
plot_de_num Source code
plot_dend Source code
plot_doublet Source code
plot_doublet_big Source code
plot_low_qc Source code
plot_pair_matrix Source code
plot_tSNE_gene Source code
plot_tSNE_meta Source code
plot_tsne_cl Source code
plot_umap_constellation Source code
plot_vg Source code
predict_annotate_cor Source code
predict_knn Source code
prepare_harmonize_big Source code
prepare_impute_genes Source code
prune_dend Source code
rcpp_get_cl_means Source code
rcpp_get_cl_means_RcppParallel Source code
rcpp_get_cl_means_RcppParallel_dense Source code
rcpp_get_cl_means_RcppParallel_transpose Source code
rcpp_get_cl_means_RcppParallel_transpose_dense Source code
rcpp_get_cl_means_dense Source code
rcpp_get_cl_means_transpose Source code
rcpp_get_cl_means_transpose_dense Source code
rcpp_get_cl_medians Source code
rcpp_get_cl_medians_RcppParallel Source code
rcpp_get_cl_medians_RcppParallel_dense Source code
rcpp_get_cl_medians_RcppParallel_transpose Source code
rcpp_get_cl_medians_RcppParallel_transpose_dense Source code
rcpp_get_cl_medians_dense Source code
rcpp_get_cl_medians_transpose Source code
rcpp_get_cl_medians_transpose_dense Source code
rcpp_get_cl_present Source code
rcpp_get_cl_present_RcppParallel Source code
rcpp_get_cl_present_RcppParallel_dense Source code
rcpp_get_cl_present_RcppParallel_transpose Source code
rcpp_get_cl_present_RcppParallel_transpose_dense Source code
rcpp_get_cl_present_dense Source code
rcpp_get_cl_present_transpose Source code
rcpp_get_cl_present_transpose_dense Source code
rcpp_get_cl_sqr_means Source code
rcpp_get_cl_sqr_means_RcppParallel Source code
rcpp_get_cl_sqr_means_RcppParallel_dense Source code
rcpp_get_cl_sqr_means_RcppParallel_transpose Source code
rcpp_get_cl_sqr_means_RcppParallel_transpose_dense Source code
rcpp_get_cl_sqr_means_dense Source code
rcpp_get_cl_sqr_means_transpose Source code
rcpp_get_cl_sqr_means_transpose_dense Source code
rcpp_get_cl_sqr_sums Source code
rcpp_get_cl_sqr_sums_RcppParallel Source code
rcpp_get_cl_sqr_sums_RcppParallel_dense Source code
rcpp_get_cl_sqr_sums_RcppParallel_transpose Source code
rcpp_get_cl_sqr_sums_RcppParallel_transpose_dense Source code
rcpp_get_cl_sqr_sums_dense Source code
rcpp_get_cl_sqr_sums_transpose Source code
rcpp_get_cl_sqr_sums_transpose_dense Source code
rcpp_get_cl_sums Source code
rcpp_get_cl_sums_RcppParallel Source code
rcpp_get_cl_sums_RcppParallel_dense Source code
rcpp_get_cl_sums_RcppParallel_transpose Source code
rcpp_get_cl_sums_RcppParallel_transpose_dense Source code
rcpp_get_cl_sums_dense Source code
rcpp_get_cl_sums_transpose Source code
rcpp_get_cl_sums_transpose_dense Source code
rd_PCA Source code
rd_PCA_big Source code
rd_WGCNA Source code
recompute_knn Source code
refine_cl Source code
reorder_big.dat_fbm Source code
reorder_big.dat_parquet Source code
reorder_cl Source code
reorder_dend Source code
rescale_samples Source code
reset_dend_label Source code
rm_genes Source code
run_consensus_clust Source code
run_iter_clust_merge Source code
sample_cells Source code
sample_cl_dat Source code
sample_cl_list Source code
sample_sets_list Source code
score_gene_mod Source code
select_N_markers Source code
select_N_markers_ds Source code
select_joint_genes Source code
select_markers Source code
select_markers_ds Source code
select_markers_groups Source code Source code
select_markers_groups_top_ds Source code
select_markers_pair Source code
select_markers_pair_direction Source code
select_markers_pair_direction_ds Source code
select_markers_pair_group Source code
select_markers_pair_group_ds Source code
select_markers_pair_group_lc Source code
select_markers_pair_group_top Source code
select_markers_pair_group_top_ds Source code
select_pos_markers Source code
select_pos_markers_ds Source code
select_top_pos_markers Source code
select_top_pos_markers_ds Source code
set_cols_fbm Source code
set_pair_matrix Source code
sim_knn Source code
simple_ebayes Source code
simple_lmFit Source code
sparse_cor Source code
standardize Source code
test_merge Source code
top_loading_genes Source code
umap_param Source code
unbranch_by_conf Source code
unbranch_by_length Source code
update_gene_score_ds Source code
update_mat_parquet_dense Source code
vec_chisq_test Source code
within_group_specific_markers Source code
z_score Source code
AllenInstitute/scrattch.bigcat documentation built on Feb. 7, 2024, 7:28 p.m.

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