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All Projects → JetBrains-Research → bioinf-commons

JetBrains-Research / bioinf-commons

Licence: MIT license
Bioinformatics library in Kotlin

Programming Languages

kotlin
9241 projects

Labels

hmmbioinformaticsprogressmethylationdatasetfastachip-seqsamplingbedbamdataframefastqmixturehypothesis-testing2bitcancellabledna-sequence

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JetBrains Research license tests

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
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