/bioinf-commons

Bioinformatics library in Kotlin.

Primary LanguageKotlinMIT LicenseMIT

License license Tests tests

Bioinf-commons

Bioinformatics library in Kotlin by JetBrains Research.

  • APIs for working with Genome, Sequence, Genes, Ontologies etc.
  • BAM, BED, FAST* formats support
  • Pandas-like data frames
  • Statistics utilities including distributions mixtures, hmms and hypothesis testing
  • Utilities for computations caching, logging, parallel execution with cancelling, etc.

Installation

The latest version of bioinf-commons is available on jCenter. If you're using Gradle just add the following to your build.gradle:

repositories {
    jcenter()
}

dependencies {
    compile 'org.jetbrains.bio:bioinf-commons:0.0.5'
}

Publishing

You can publish a new release with a one-liner

./gradlew clean assemble test generatePomFileForMavenJavaPublication bintrayUpload

Make sure to set Bintray credentials (see API key section here) in $HOME/.gradle/gradle.properties.

$ cat $HOME/.gradle/gradle.properties
bintrayUser=CHANGEME
bintrayKey=CHANGEME