bioframe

Bioframe is a library to enable flexible and scalable operations on genomic interval dataframes in python. Building bioframe directly on top of pandas enables immediate access to a rich set of dataframe operations. Working in python enables rapid visualization and iteration of genomic analyses.

Guide

• Quickstart
• Genomic interval operations
• Reading genomic dataframes
• Performance
• How do I
• Definitions
• Specifications

Tutorials

• How to: assign TF Motifs to ChIP-seq peaks
• How to: assign ChIP-seq peaks to genes

API

• Construction
  • from_any()
  • from_dict()
  • make_viewframe()
  • sanitize_bedframe()
• Validation
  • is_bedframe()
  • is_cataloged()
  • is_contained()
  • is_covering()
  • is_overlapping()
  • is_sorted()
  • is_tiling()
  • is_viewframe()
• Interval operations
  • assign_view()
  • closest()
  • cluster()
  • complement()
  • count_overlaps()
  • coverage()
  • expand()
  • merge()
  • overlap()
  • select()
  • select_indices()
  • select_labels()
  • select_mask()
  • setdiff()
  • sort_bedframe()
  • subtract()
  • trim()
• File I/O
  • load_fasta()
  • read_bam()
  • read_bigbed()
  • read_bigwig()
  • read_chromsizes()
  • read_pairix()
  • read_tabix()
  • read_table()
  • to_bigbed()
  • to_bigwig()
• Resources
  • Genome assembly metadata
    • assemblies_available()
    • assembly_info()
    • GenomeAssembly
  • Remote resources
    • fetch_centromeres()
    • fetch_chromsizes()
• Additional tools
  • binnify()
  • digest()
  • frac_gc()
  • frac_gene_coverage()
  • frac_mapped()
  • make_chromarms()
  • pair_by_distance()
  • seq_gc()
• Plotting
  • plot_intervals()
  • to_ucsc_colorstring()
• Low-level API
  • Array operations
    • arange_multi()
    • closest_intervals()
    • interweave()
    • merge_intervals()
    • overlap_intervals()
    • overlap_intervals_outer()
    • sum_slices()
  • Specifications
    • is_chrom_dtype()
    • specs._verify_column_dtypes()
    • specs._verify_columns()
    • specs._get_default_colnames()
  • String operations
    • is_complete_ucsc_string()
    • parse_region()
    • parse_region_string()
    • to_ucsc_string()

Indices and tables

• Index

• Module Index

• Search Page