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blaseRtools

This R package includes commonly used functions for R analysis in the Blaser Lab.

Installation

You can install the latest version of blaseRtools with:

# using base function
install.packages('blaseRtools', repos = c('https://blaserlab.r-universe.dev', 'https://cloud.r-project.org'))

# or if using blaseRtemplates function
blaseRtemplates::install_one_package("blaseRtools", "new")

Useage

All commonly used functions for the end user are prefixed “bb_”. If you load the blaseRtools package and supporting data with

Then if you run ``library(“blaseRtools”)``` you can access functions by typing “bb_” and an autocomplete window with selections should pop up.

Functions related to the “Ape” and “Trace” classes are prefixed “Ape.” and “Trace.”, respectively.

Function Modules

All functions are documented and have help pages which can be reviewed after installation. Tutorials describing typical use-cases for each module of functions are linked when available.

  • scRNA-seq
    • bb_align
    • bb_annotate_npc
    • bb_cellmeta
    • bb_cluster_representation
    • bb_doubletfinder
    • bb_gene_dotplot
    • bb_gene_modules
    • bb_gene_pseudotime
    • bb_gene_umap
    • bb_gene_violinplot
    • bb_goenrichment
    • bb_gosummary
    • bb_load_tenx_targz
    • bb_monocle_regression
    • bb_pseudobulk_mf
    • bb_qc
    • bb_rejoin
    • bb_rowmeta
    • bb_seurat_anno
    • bb_triplecluster
    • bb_var_umap
  • Ape class: Programmatic methods for working with genbank files.
    • Ape.DNA
    • Ape.fasta
    • Ape.fimo
    • Ape.granges
    • Ape.save
    • Ape.setFeatures
    • bb_parseape
    • bb_make_ape_genomic
    • bb_make_ape_transcript
  • Trace class: A container for working with range-based data from ATAC and ChIP-seq experiments.
    • bb_buff_granges
    • bb_makeTrace
    • bb_merge_narrowpeaks
    • bb_metafeature
    • bb_plot_trace_axis
    • bb_plot_trace_data
    • bb_plot_trace_feature
    • bb_plot_trace_links
    • bb_plot_trace_model
    • bb_plot_footprint
    • bb_promoter_overlap
    • bb_read_bam
    • bb_read_narrowpeak
    • Trace.data
    • Trace.features
    • Trace.gene_model
    • Trace.links
    • Trace.plot_range
    • Trace.setFeatures
    • Trace.setLinks
    • Trace.setRange
  • Image blinding for quantitative analysis
    • bb_blind_images
    • bb_unblind_images