Awesome Scala

Bioinformatics

bigdatagenomics/adam

ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.

Scala versions: 2.10 2.11 2.12

parquet genomics big-data java avro spark scala python r bioinformatics

967 304 66
fulcrumgenomics/fgbio

Tools for working with genomic and high throughput sequencing data.

Scala versions: 2.11 2.12 2.13

genomics scala molecular-indexes fgbio umi ngs analyzing-genomic-data bioinformatics

304 68 28 15
projectglow/glow

An open-source toolkit for large-scale genomic analysis

Scala versions: 2.11 2.12

genomics gwas spark delta regression machine-learning population-genetics

258 106 24
clulab/reach

Reach Biomedical Information Extraction

Scala versions: 2.11 2.12

96 38 17
bigdatagenomics/cannoli

Distributed execution of bioinformatics tools on Apache Spark. Apache 2 licensed.

Scala versions: 2.10 2.11 2.12

38 17 4
aehrc/variantspark

machine learning for genomic variants

Scala versions: 2.11 2.12

notebook variant-spark emr gwas variantspark random-forest genome association-studies bioinformatics vcf databricks aws

138 44 9
darrenjw/scala-smfsb

Scala library for biochemical network simulation, associated with the 3rd edition of the textbook Stochastic Modelling for Systems Biology

Scala versions: 2.11 2.12 2.13 3.x

12 2 1
pityka/pairwisealignment

pairwise sequence alignment in scala

Scala versions: 2.12 2.13 3.x

Scala.js versions: 1.x

needleman-wunsch scala smith-waterman-gotoh wavefront-alignment

3 1 2