Man pages for hesselberthlab/scrunchy
Single Cell Reconstruction of Functional Heterogeneity

add_labelAdds useful labels to colData.
add_statsAdd stats to plot activities per cluster
calc_cell_cycleCalculate cell-cycle assignments
calc_hairpin_coverageCalculate coverage across hairpins
calc_pcaCalculate principal components using irlba
calc_qvaluesCalculate q-values
calc_tsneGenerate 2D cell embeddings using tSNE
calc_umapGenerate 2D cell embeddings using UMAP
calc_var_featuresCalculate variable features
clr_normalizeCentered log-ratio normalize a matrix
cluster_kmeansRun k-means clustering algorithm
cluster_leidenRun Leiden clustering algorithm
create_fsceCreate a functional single-cell experiment
create_sce_featureCreate a single-cell feature experiment
create_sce_haircutCreate a single-cell Haircut experiment
create_sce_rnaseqCreate a single-cell mRNA-seq experiment
filter_matrixFilter and write a sparseMatrix keeping only specified...
filter_moleculesFilter barcodes in molecule file and write to disk
fsce_smallAn example FunctionalSingleCellExperiment
fsce_tidyTidied tibble of data from fsce_small
FunctionalSingleCellExperimentConstructor for a 'FunctionalSingleCellExperiment' object
FunctionalSingleCellExperiment-classAn S4 class to represent a functional single cell experiment
human_gene_idsHuman gene identifiers
is.molecule_dfTest if the object is a molecule_df.
log_normalizeLog-normalize a matrix
molecule_dfdata.frame that contains molecule info
normalizeNormalize data in a SingleCellExperiment
palette_OkabeItoColor palette proposed by Okabe and Ito
pbmc_marker_genesComman human PBMC marker genes
plot_activityPlot activities per cluster
plot_barcodesPlot UMI count distribution for barcodes
plot_dimsScatter plot of cells in a two-dimensional embedding.
plot_dims_multiPlot multiple 2D plots in a grid
plot_hairpin_coveragePlot coverage across hairpins
plot_heatmapHeatmap of signals
plot_pcvariancePlot PCA variance
plot_saturationPlot sequencing saturation
read_matrixLoad mtx formatted 10x or haircut matrices
read_moleculesRead molecule file into memory
scale_OkabeItoOkabe-Ito color scale
scrunchyscrunchy: single-cell reconstruction of functional...
scrunchy_dataProvide path to scrunchy internal data
stat_activity_groupedCompare activity differences between groups.
stat_anova_groupedAnalysis of variance of activities across groups
stat_anova_tukeyPost-hoc analysis of ANOVA results
tidy_allTidy all
tidy_coldataTidy colData
tidy_countsTidy counts data
tidy_dimsTidy reducedDims data
tidy_logcountsTidy logcounts data
tidy_stats_groupedTidy grouped statistics
umitools_to_mtxConvert umitools flat format tsv to sparseMatrix .mtx format
write_matrixWrite a sparseMatrix to disk
hesselberthlab/scrunchy documentation built on Nov. 11, 2019, 2:29 p.m.