API for MarioniLab/scran
Methods for Single-Cell RNA-Seq Data Analysis

Global functions
DM Man page Source code
SCE_subset_genes Source code
SCEs_to_matrices Source code
add_log_values Source code
adjust.shift.variance Source code
average_correction Source code
batch_rescaler Source code
buildKNNGraph Man page Source code
buildKNNGraph,ANY-method Man page
buildKNNGraph,SingleCellExperiment-method Man page
buildSNNGraph Man page Source code
buildSNNGraph,ANY-method Man page
buildSNNGraph,SingleCellExperiment-method Man page
calc_residuals_wt_zeroes Source code
center_along_batch_vector Source code
centered_SVD Source code
check_batch_consistency Source code
check_centered_SF Source code
check_null_dist Source code
check_spike_consistency Source code
choose_gene_names Source code
choose_leftright_pvalues Source code
clusterModularity Man page Source code
combineVar Man page Source code
combine_pvalues Source code
compute.correction.vectors Source code
computeSpikeFactors Man page
computeSpikeFactors,SingleCellExperiment-method Man page
computeSumFactors Man page Source code
computeSumFactors,ANY-method Man page
computeSumFactors,SingleCellExperiment-method Man page
compute_intra_var Source code
construct_pair_indices Source code
convertTo Man page
convertTo,SingleCellExperiment-method Man page
convert_to Source code
correlateNull Man page Source code
correlatePairs Man page
correlatePairs,ANY-method Man page
correlatePairs,SingleCellExperiment-method Man page
correlate_pairs Source code
cosineNorm Man page Source code
create_full_stats Source code
create_linear_system Source code
create_output_container Source code
create_var_df Source code
cyclone Man page Source code
cyclone,ANY-method Man page
cyclone,SingleCellExperiment-method Man page
decomposeVar Man page
decomposeVar,ANY,list-method Man page
decomposeVar,SingleCellExperiment,list-method Man page
decompose_var Source code
define_first_merge Source code
define_next_merge Source code
delayed_crossprod Source code
delayed_mult Source code
denoisePCA Man page Source code
denoisePCA,ANY-method Man page
denoisePCA,SingleCellExperiment-method Man page
doubletCells Man page
doubletCells,ANY-method Man page
doubletCells,SingleCellExperiment-method Man page
doubletCluster Man page
doubletCluster,ANY-method Man page
doubletCluster,SingleCellExperiment-method Man page
doublet_cells Source code
doublet_cluster Source code
extract_weightings Source code
fastMNN Man page Source code
fast_svd Source code
find.markers Source code
find.mutual.nn Source code
find.shared.subspace Source code
findMarkers Man page Source code
findMarkers,ANY-method Man page
findMarkers,SingleCellExperiment-method Man page
find_largest_col Source code
find_overlap_exprs Source code
fit_linear_model Source code
fit_lm_internal Source code
fit_oneway Source code
generateSphere Source code
get.bio.span Source code
get_correlation Source code
get_log_offset Source code
get_nls_starts Source code
get_npcs_to_keep Source code
get_phase_score Source code
get_t_test_stats Source code
get_var_stats Source code
guess_lower_bound Source code
improvedCV2 Man page
improvedCV2,ANY-method Man page
improvedCV2,SingleCellExperiment-method Man page
keep_rank_in_range Source code
limit_cluster_size Source code
logBH Source code
makeTechTrend Man page Source code
merge_closest_graph Source code
mnnCorrect Man page Source code
mprovedCV2 Source code
multiBatchNorm Man page Source code
multiBatchPCA Man page Source code
multiBlockNorm Man page Source code
multiBlockVar Man page Source code
multi_pca Source code
overlapExprs Man page Source code
overlapExprs,ANY-method Man page
overlapExprs,SingleCellExperiment-method Man page
parallelPCA Man page Source code
parallelPCA,ANY-method Man page
parallelPCA,SingleCellExperiment-method Man page
parallel_PA Source code
per_cluster_normalize Source code
prepare.input.data Source code
prepare_cv2_data Source code
prepare_overlap_output Source code
quickCluster Man page
quickCluster,ANY-method Man page
quickCluster,SingleCellExperiment-method Man page
quick_cluster Source code
rank_top_genes Source code
ranksafe_qr Source code
rescale_clusters Source code
run_stouffer Source code
run_t_test Source code
s_sig_limited Source code
sandbag Man page
sandbag,ANY-method Man page
sandbag,SingleCellExperiment-method Man page
setup_knn_data Source code
setup_loess_args Source code
setup_nls_args Source code
setup_spline_args Source code
spawn_doublet_pcs Source code
spike_subset Source code
split_matrix_by_workers Source code
split_vector_by_workers Source code
subset_to_index Source code
subtract.bio Source code
svd_internal Source code
svd_to_lowrank Source code
svd_to_pca Source code
technicalCV2 Man page Source code
technicalCV2,ANY-method Man page
technicalCV2,SingleCellExperiment-method Man page
testVar Man page Source code
test_block_internal Source code
trendVar Man page
trendVar,ANY-method Man page
trendVar,SingleCellExperiment-method Man page
trend_var Source code
tricube_weighted_correction Source code
tricube_weighted_remapping Source code
weighted_average_vals Source code
worker_assign Source code
MarioniLab/scran documentation built on Aug. 15, 2018, 5:32 a.m.