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All functions

Ape-class Ape
An S4 class to hold genebank/APE file data.
Ape.DNA()
Get the DNASringSet Slot from an Ape Object
Ape.fasta()
Save an Ape Instance as a Fasta File
Ape.fimo()
Run FIMO on Selected Ape Object Features
Ape.granges()
Get the GRanges Slot from an Ape Object
Ape.save()
Save an Ape Instance as a Genebank Format File
Ape.setFeatures()
Set the FEATURES Slot of a GRanges Object
COMMENTS()
Get the Comments Slot from an Ape Object
FEATURES()
Get the Features Slot from an Ape Object
LOCUS()
Get the Locus Slot from an Ape Object
LearnGraph()
Run link[monocle3]{learn_graph} on a Seurat object
blaseRtools blaseRtools-package SeuratWrappers-package
blaseRtools: R Tools for Blaser Lab Data Analysis
Trace-class Trace
An S4 class to Hold Genome Track Data
Trace.data()
Get the Trace Data Slot from a Trace Object
Trace.gene_model()
Get the gene_model Slot from a Trace Object
Trace.links()
Get the Links Slot from a Trace Object
Trace.peaks()
Get the peaks Slot from a Trace Object
Trace.plot_range()
Get the plot_range Slot from a Trace Object
Trace.setData()
Set the Trace Data Slot of a GRanges Object
Trace.setLinks()
Set the Links Slot of a GRanges Object
Trace.setRange()
Set the Plot Range Slot of a GRanges Object
Trace.setpeaks()
Set the peaks Slot of a GRanges Object
add_cds_factor_columns()
Add predefined sample-level cell metadata to cell data sets while importing
aggregate(<Matrix>)
Compute summary statistics of a Matrix
as.Seurat(<cell_data_set>)
Convert single cell experiment to Seurat
as.cell_data_set()
Convert objects to Monocle3 cell_data_set objects
bb_aggregate()
Aggregate Single Cell Gene Expression
bb_align()
Align a CDS object according to a metadata variable
bb_annotate_npc()
Annotate a Plot using NPC Coordinates
bb_blind_images()
Make a Copy of Image Files and Rename With File Hashes in Blinded Folder
bb_buff_granges()
Clean Up Your GRanges Object
bb_cds_anno()
Annotate a CDS by Label Transfer
bb_cds_heatmap()
Make a Heatmap of Aggregated Gene Expressionf from a CDS
bb_cellchat()
Infer Cell-Cell Communication
bb_cellchat_heatmap()
Make a Complex Heatmap From a CellChat Object With Sensible Defaults
bb_cellmeta()
Get Cell Metadata
bb_cite_umap()
Plot a UMAP Showing Cite-Seq Antibody Binding
bb_cluster_representation()
Cluster Representation By Fisher Exact Test Per Cell
bb_cluster_representation2()
Cluster Representation By Regression Per Sample
bb_daseq()
Calculate Differential Abundance Using DAseq
bb_doubletfinder()
Use doubletfinder to model and mark doublets
bb_extract_msig()
Extract MSIGDB Gene Sets
bb_fix_file_path()
Convert windows filepath to linux-compatible.
bb_fragment_replacement()
Replace The Path to a Fragment File In a Signac Object
bb_gene_dotplot()
Make a dotplot of gene expression by cell population
bb_gene_modules()
A function to generate gene modules and add them to the Gene Metadata
bb_gene_pseudotime()
Plot expression of a gene or genes in pseudotime.
bb_gene_umap()
Make a Plot of Gene Expression in UMAP Form
bb_gene_violinplot()
Make a plot of gene expression in UMAP form
bb_genebubbles()
Create a Gene Bubble/Dot Plot
bb_goenrichment()
Go Term Enrichment
bb_goscatter()
Make a scatter plot of GO term associations
bb_gosummary()
A function to reduce go terms by semantic similarity
bb_load_tenx_h5()
Load a 10X Genomics H5 File and Return a CDS
bb_load_tenx_targz()
Load 10X Data Into CDS
bb_loupeR()
Create a Loupe File from a Cell Data Set
bb_makeTrace()
Construct a Trace object from a Signac Object or Granges object
bb_make_ape_genomic()
Make an Ape Genome Object
bb_make_ape_transcript()
Make an Ape Transcriptome Object
bb_merge_narrowpeaks()
A Function To Merge Replicate Narrow Peaks GRanges
bb_metafeature()
A Function to Generate Data For Making MetaPlots
bb_monocle_regression()
A function to perform regression on single cell data.
bb_monocle_regression_better()
An Improved Function to Perform Regression on Single Cell Data.
bb_parseape()
Parse a Genebank File and Construct an APE Object
bb_plot_genes_in_pseudotime()
Plots expression for one or more genes as a function of pseudotime
bb_plot_rowData_col()
A helper function to generate a data frame in the proper form for aggregate expression plotting with bb_gene_umap.
bb_plot_trace_axis()
Plot The X Axis From A Trace Object
bb_plot_trace_data()
Plot The Trace Data From A Trace Object
bb_plot_trace_links()
Plot The Link Data From A Trace Object
bb_plot_trace_model()
Plot The Gene Model From A Trace Object
bb_plot_trace_peaks()
Plot The peak Data From A Trace Object
bb_plotfootprint()
Plot motif footprinting results
bb_print_full_stats()
Print out a stats report
bb_promoter_overlap()
Calculate The Overlap Between Peaks and Promoters
bb_pseudobulk_mf()
Run Multifactor Pseudobulk Analysis using Deseq2
bb_pseudotime()
Learn Graph and Calculate Pseudotime
bb_qc()
A function to run qc tests on cds objects.
bb_read_bam()
Read Bam Files
bb_read_narrowpeak()
A Function to Read In Narrow Peaks Files
bb_rejoin()
Rejoin qc and doubletfinder data to a cds object
bb_remove_dupes()
Remove rows that have duplicates in a given column
bb_rowmeta()
Get Feature/Gene Metadata
bb_seurat_anno()
A function to generate automated cell labelings with Seurat
bb_split_atac()
Split Out Peaks Data
bb_split_citeseq()
Split Antibody Capture Data into Alt Experiment
bb_tbl_to_coldata()
A Function To Add Tibble Columns To Cell Metadata
bb_tbl_to_matrix()
Convert a wide-form tibble a matrix
bb_tbl_to_rowdata()
A Function To Add Tibble Columns To Feature Metadata
bb_triplecluster()
A function to generate clusters from scRNA-seq data
bb_unblind_images()
Rejoin Blinded Scores to Original File Names
bb_var_umap()
A function to generate a UMAP with colors mapped to colData variables
dMcast()
Casts or pivots a long data frame into a wide sparse matrix
data_median_se()
Generate median +/- se stat object for jitter ggplot
data_summary_mean_sd()
Generate mean +/- sd stat object for jitter ggplot
data_summary_mean_se()
Generate mean +/- se stat object for jitter ggplot
data_summary_median_iqr()
Generate median +/- iqr stat object for jitter ggplot
data_summary_median_mad()
Generate median +/- mad stat object for jitter ggplot
filter_cds()
Filter a CDS
geom_split_violin()
geom_split_violin
granges_to_features()
Format a GRanges Object as a Character Vector For Inclusion in Genebank File
`%notin%`
Operators
merge.Matrix() join.Matrix()
Merges two Matrices or matrix-like objects
normalize_batch()
Noramalize a Data Table by Group and Batch
rBind.fill()
Combine matrixes by row, fill in missing columns
se()
Calculate standard error of the mean
show(<Ape>)
Show an Ape Object
show(<Trace>)
Show a Trace Object