HTSeq: Analysing high-throughput sequencing data with Python

• Overview
  • Documentation overview
  • Author
  • License
• Prequisites and installation
  • Prequisites
  • Download
  • Installing a binary package
  • Installing a source package
• A tour through HTSeq
  • Reading in reads
  • Genomic intervals and genomic arrays
  • Calculating coverage vectors
  • Counting reads by genes
  • Mapping structural variants to genes
  • And much more
• A detailed use case: TSS plots
  • Using the full coverage
  • Using indexed BAM files
  • Streaming through all reads
• Sequences and FASTA/FASTQ files
  • Sequence
  • SequenceWithQualities
  • FastaReader
  • FastqReader
• Genomic intervals and genomic arrays
  • GenomicInterval
  • GenomicPosition
  • GenomicArray
  • GenomicArrayOfSets
• Read alignments
  • Concepts
  • Parser classes
  • Alignment and AlignmentWithSequenceReversal
  • Format-specific Alignment classes
  • Multiple alignments
  • CIGAR strings
• Features
  • GFF_Reader and GenomicFeature
  • VCF_Reader and VariantCall
• Miscellaneous
  • FileOrSequence
  • Version
• Quality Assessment with htseq-qa
  • Plot
  • Usage
• Counting reads in features with htseq-count
  • Usage
• Version history
  • Version 0.5.3
  • Version 0.5.2
  • Version 0.5.1
  • Version 0.5.0
  • Version 0.4.7
  • Version 0.4.6
  • Version 0.4.5
  • Version 0.4.4
  • Version 0.4.3
  • Version 0.4.2
  • Version 0.4.1
  • Version 0.4.0
  • Version 0.3.7
• Notes for Contributers
  • Source code
  • Languages
  • Build process
  • Distributing
  • Files

• Index