https://github.com/jetbrains-research/bioinf-commons

Bioinformatics library in Kotlin
https://github.com/jetbrains-research/bioinf-commons

2bit bam bed bioinformatics cancellable chip-seq dataframe dataset dna-sequence fasta fastq hmm hypothesis-testing kotlin methylation mixture progress sampling

Last synced: 7 months ago
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Bioinformatics library in Kotlin

• Host: GitHub
• URL: https://github.com/jetbrains-research/bioinf-commons
• Owner: JetBrains-Research
• License: mit
• Created: 2019-03-02T20:15:30.000Z (over 6 years ago)
• Default Branch: master
• Last Pushed: 2024-09-12T17:10:21.000Z (9 months ago)
• Last Synced: 2024-09-13T19:59:41.606Z (9 months ago)
• Topics: 2bit, bam, bed, bioinformatics, cancellable, chip-seq, dataframe, dataset, dna-sequence, fasta, fastq, hmm, hypothesis-testing, kotlin, methylation, mixture, progress, sampling
• Language: Kotlin
• Homepage:
• Size: 2.43 MB
• Stars: 31
• Watchers: 14
• Forks: 3
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGES.txt
  • License: LICENSE.txt

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README

        
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Bioinf-commons

==============

Bioinformatics library in [Kotlin](https://kotlinlang.org).

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

-----

   ```bash

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

   ```

Usages

------

Used in the following projects:

* [SPAN](https://github.com/JetBrains-Research/span) Semi-supervised Peak Analyzer

* [JBR](https://github.com/JetBrains-Research/jbr) JBR Genome Browser

* [FARM](https://github.com/JetBrains-Research/fishbone) hierarchical association rule mining and visualization method