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

Global functions
DM Man page Source code
SCE_subset_genes Source code
add_log_values Source code
adjust.shift.variance Source code
bpl.get.knnx 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
check_centered_SF Source code
check_null_dist 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
construct_pair_indices Source code
convertTo Man page
convertTo,SingleCellExperiment-method Man page
convert_to Source code
convert_to_output Source code
correlateNull Man page Source code
correlatePairs Man page
correlatePairs,ANY-method Man page
correlatePairs,SingleCellExperiment-method Man page
correlate_pairs Source code
cosine.norm 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
denoisePCA Man page Source code
denoisePCA,ANY-method Man page
denoisePCA,SingleCellExperiment-method Man page
extract_weightings 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_knn Source code
find_largest_col Source code
find_overlap_exprs Source code
fit_linear_model Source code
fit_lm_internal Source code
fit_oneway Source code
full_svd 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
make_var_defaults Source code
merge_closest_graph Source code
mnnCorrect Man page Source code
mprovedCV2 Source code
multiBlockVar Man page 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
rlba_svd 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
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
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
weighted_average_vals Source code
worker_assign Source code
MarioniLab/scran documentation built on May 20, 2018, 10:24 p.m.