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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
show(<Image_>) file_path() `file_path<-`() species() `species<-`() stage() `stage<-`() genetics() `genetics<-`() treatment() `treatment<-`() microscope() `microscope<-`() mag() `mag<-`() filter() `filter<-`() use() `use<-`() note() `note<-`()
An S4 Class for Holding Image Metadata
show(<ImageCatalog>) `[`(<ImageCatalog>,<ANY>,<ANY>,<ANY>) `[[`(<ImageCatalog>,<ANY>,<ANY>) `$`(<ImageCatalog>) ImageCatalog.as_tibble() ImageCatalog.write() ImageCatalog.add() ImageCatalog.delete()
An S4 Image Catalog
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_import_seacr_peaks()
Import Peaks from SEACR
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_() bb_monocle_anno() bb_monocle_project()
Annotate Single cell Data Using Monocle3
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_pseudocells()
Generate a CDS from Bulk RNA-seq data
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