bioinf-commons
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Bioinformatics library in Kotlin
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: