bionumpy

Home

  • BioNumPy at a glance
  • Getting started with BioNumPy in 10 minutes
  • Using BioNumPy in your existing project

Tutorials

  • Filtering FASTQ reads
  • Working with BAM-files
  • Getting read pileup inside peaks (intervals)
  • FastQC-like quality-checking of FASTQ files
  • Computing GC content inside genes
  • Position Weight Matrix
  • Simulating sequence datasets
  • Computing the similarity between two BED-files
  • Extracting kmers around snps

Interoperability

  • Numpy Interoperability
  • Using BioNumPy with Biopython
  • Pandas Interoperability

BioNumPy Concepts

  • Reading files
  • Encodings
  • Supported file formats
  • Reading a new file format
  • Sequences
  • Intervals
  • Working with Multiple Files/Data Sources
  • Broadcastable Functions

API documentation

  • BnpDataclass
  • Genome arithmetics
  • Genomic Data
  • IO
  • Sequences
  • Streams

Other

  • Developer guide
  • BioNumPy manuscript
bionumpy
  • Overview: module code

All modules for which code is available

  • bionumpy.arithmetics.intervals
  • bionumpy.arithmetics.similarity_measures
  • bionumpy.bnpdataclass.bnpdataclass
  • bionumpy.bnpdataclass.bnpdataclassfunction
  • bionumpy.genomic_data.annotation
  • bionumpy.genomic_data.genome
  • bionumpy.genomic_data.genomic_intervals
  • bionumpy.genomic_data.genomic_sequence
  • bionumpy.genomic_data.genomic_track
  • bionumpy.io.delimited_buffers
  • bionumpy.io.fastq_buffer
  • bionumpy.io.files
  • bionumpy.io.indexed_fasta
  • bionumpy.io.indexed_files
  • bionumpy.io.one_line_buffer
  • bionumpy.io.vcf_buffers
  • bionumpy.sequence.count_encoded
  • bionumpy.sequence.kmers
  • bionumpy.sequence.minimizers
  • bionumpy.sequence.position_weight_matrix
  • bionumpy.sequence.string_matcher
  • bionumpy.streams.decorators

© Copyright 2021, Knut Rand.

Built with Sphinx using a theme provided by Read the Docs.