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
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© Copyright 2021, Knut Rand.

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