Create Objects

create_fsce()

Create a functional single-cell experiment

create_sce_haircut()

Create a single-cell Haircut experiment

create_sce_rnaseq()

Create a single-cell mRNA-seq experiment

Format and Normalize Data

tidy_all()

Tidy all

tidy_coldata()

Tidy colData

tidy_counts()

Tidy counts data

tidy_dims()

Tidy reducedDims data

tidy_logcounts()

Tidy logcounts data

tidy_stats_grouped()

Tidy grouped statistics

clr_normalize()

Centered log-ratio normalize a matrix

log_normalize()

Log-normalize a matrix

normalize()

Normalize data in a SingleCellExperiment

Analyze Data

calc_cell_cycle()

Calculate cell-cycle assignments

calc_hairpin_coverage()

Calculate coverage across hairpins

calc_pca()

Calculate principal components using irlba

calc_qvalues()

Calculate q-values

calc_tsne()

Generate 2D cell embeddings using tSNE

calc_umap()

Generate 2D cell embeddings using UMAP

calc_var_features()

Calculate variable features

cluster_kmeans()

Run k-means clustering algorithm

cluster_leiden()

Run Leiden clustering algorithm

stat_activity_grouped()

Compare activity differences between groups.

stat_anova_grouped()

Analysis of variance of activities across groups

stat_anova_tukey()

Post-hoc analysis of ANOVA results

Visualize Data

plot_activity()

Plot activities per cluster

plot_barcodes()

Plot UMI count distribution for barcodes

plot_dims()

Scatter plot of cells in a two-dimensional embedding.

plot_dims_multi()

Plot multiple 2D plots in a grid

plot_hairpin_coverage()

Plot coverage across hairpins

plot_heatmap()

Heatmap of signals

plot_saturation()

Plot sequencing saturation

Sample Data Sets

fsce_small

An example FunctionalSingleCellExperiment

fsce_tidy

Tidied tibble of data from fsce_small

pbmc_marker_genes

Comman human PBMC marker genes

human_gene_ids

Human gene identifiers

Object Definitions

FunctionalSingleCellExperiment-class

An S4 class to represent a functional single cell experiment

FunctionalSingleCellExperiment()

Constructor for a FunctionalSingleCellExperiment object

Utilities

install_py_deps()

Install python dependencies for cluster_leiden.

molecule_df()

data.frame that contains molecule info

is.molecule_df()

Test if the object is a molecule_df.

filter_molecules()

Filter barcodes in molecule file and write to disk

umitools_to_mtx()

Convert umitools flat format tsv to sparseMatrix .mtx format

read_matrix()

Load mtx formatted 10x or haircut matrices

read_molecules()

Read molecule file into memory

filter_matrix()

Filter and write a sparseMatrix keeping only specified barcodes

write_matrix()

Write a sparseMatrix to disk

scrunchy

scrunchy: single-cell reconstruction of functional heterogeneity

scrunchy_data()

Provide path to scrunchy internal data

palette_OkabeIto palette_OkabeIto_black

Color palette proposed by Okabe and Ito

scale_color_OkabeIto() scale_fill_OkabeIto() scale_OkabeIto()

Okabe-Ito color scale