Package index • aquarius

scRNA-Seq data handling

add_cell_cycle(): Cell cycle phase prediction

cell_annot_custom(): Cell type annotation with Seurat::AddModuleScore

filter_features(): Features filtering based criteria

find_doublets(): Find cell doublets

integration_fastmnn(): Run fastMNN

load_sc_data(): Load scRNA-Ses count matrix into a Seurat object

run_diffusion_map(): Generate a diffusion map

Trajectory

traj_tinga(): Trajectory inference with TInGa

traj_inference(): Trajectory inference

Copy Number

cnv_add_score(): Add peak score in Seurat object

cnv_compute_intensity(): Compute CNV intensity of gain or loss

cnv_find_peak(): Find peaks in CNV table

cnv_label_peaks(): Find peaks in CNV table

cnv_plot_heatmap(): Plot heatmap of CNV results

cnv_plot_intensity(): Plot intensity of gain or loss

cnv_show_peaks(): Find peaks in CNV table

read_infercnv(): Read infercnv table

Functional enrichment

get_gene_sets(): Get gene sets

run_enrichr(): clusterProfiler::enricher wrapper

run_gsea(): Run GSEA using clusterProfiler::GSEA

Visualization

plot_alluvial(): Alluvial plot

plot_barplot(): Plot a bar plot

plot_c30_palette(): Visualization of the c30_palette

plot_df(): Plot a dataframe

plot_dotplot(): Dotplot for markers by cell type

plot_doublets_composition(): Plot doublet composition

plot_empty(): Make empty plot

plot_external(): Plot external information on a feature plot

plot_gsea_barplot(): Plot the GSEA plot (NES)

plot_gsea_curve(): Plot the GSEA curve

plot_label_dimplot(): Label some cells on a 2D plot

plot_pct(): Plot Seurat::FindMarkers result

plot_piechart(): Plot a piechart

plot_piechart_subpopulation(): Titre

plot_prop_heatmap(): Plot heatmap showing proportions

plot_qc_density(): Plot a metric distribution density and histogram

plot_qc_facslike(): Plot a point cloud and marginal distributions

plot_red_and_blue(): Plot cells with two colors

plot_selector(): Plot selector

plot_split_dimred(): Dimension plot with background

plot_subpopulation(): Plot a subset of cells

plot_violin(): Plot violin plot

plot_wordcloud(): Plot a wordcloud

Utilities

create_parallel_instance(): Multithreading cluster

find_extrema_curve(): Find extrema of a curve

find_extrema_density(): Find extrema of a distribution

find_features_order(): Find features order, for a heatmap

gg_color_hue(): ggplot default colors

prepare_gsea(): Prepare GSEA

print_to_copy_paste(): Print to copy paste

read_gtf(): Read GTF file

repro_dependency_tree(): Get exhaustive list of packages with there dependencies

repro_installation_order(): Get installation order to install packages such as no dependencies need to be installed

run_rescale(): Rescale vector

sample_cell_barcode(): Generate a sampled Seurat object

Data

cc.genes: Cell cycle genes

cc.pairs: Cell cycle genes pairs

c30_palette: A vector of 30 distinct colors

palette_BlWhRd: A palette to from blue to white to red

palette_GrOrBl: A palette to from gray to orange to black