Package index
-
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 aSeurat
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