Awesome Scala

Bioinformatics

bigdatagenomics/adam 0.23.0

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

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

1003 308 66
fulcrumgenomics/fgbio 2.4.0

Tools for working with genomic and high throughput sequencing data.

Scala versions: 2.13

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

315 67 17
projectglow/glow 2.0.0

An open-source toolkit for large-scale genomic analysis

Scala versions: 2.12

genomics gwas spark delta regression machine-learning population-genetics

272 111 26
clulab/reach 1.6.2

Reach Biomedical Information Extraction

Scala versions: 2.11 2.12

97 39 17
bigdatagenomics/cannoli 1.0

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

Scala versions: 2.12

39 17 4
aehrc/variantspark 0.5.2

machine learning for genomic variants

Scala versions: 2.12

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

140 45 9
darrenjw/scala-smfsb 1.0

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

Scala versions: 2.13 3.x

12 3 1
pityka/pairwisealignment 2.2.7

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