Bioinf-commons

Bioinformatics library in Kotlin.

Contents

• org.jetbrains.bio.dataframe - Pandas like dataframe
• org.jetbrains.bio.experiment - Named computation - experiment and resources configuration
• org.jetbrains.bio.genome - APIs for working with Genome, Sequence, Genes, Ontologies etc.
  • containers - Genome location sets API
  • coverage - Genome coverage API, paired/single end, fragment size estimation
  • data - Describe any kind of dataset resources including replicates
  • format - Bam (including Bisulfite sequencing), Bed, Fasta, Fastq, 2bit formats support
  • methylome - API to work with methylomes - filtration, statistics, aggregations etc.
  • query - Named functions - queries with caching capabilities
  • sampling - API for genomic sampling - sequencies, locations, etc.
  • sequence - Genome sequence API
    Also: Biomart, Ensembl, UCSC support, Genomes and Genes annotations
• org.jetbrains.bio.statistics - Statistics utilities including distributions mixtures, hmms and hypothesis testing
• org.jetbrains.bio.util - Cancellable computations, progress reporters, logging utilities, and other utils

Tests

$ ./gradlew clean test --no-daemon --max-workers 1

Usages

Used in the following projects:

• SPAN Semi-supervised Peak Analyzer
• JBR JBR Genome Browser
• FARM hierarchical association rule mining and visualization method