Pinned Repositories
adam
A genomics processing engine and specialized file format built using Apache Avro, Apache Spark and Parquet. Apache 2 licensed.
avocado
A Variant Caller, Distributed. Apache 2 licensed.
bam2fastq
Bam to Fastq processing using Toil
bcbio-nextgen
Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
bdg-convert
Conversions to and from Big Data Genomics Avro Formats. Apache 2 licensed.
bdg-convert-ga4gh
Conversions between GA4GH Protobuf and Big Data Genomics Avro Formats. Apache 2 licensed.
bdg-formats
Open source formats for scalable genomic processing systems using Avro. Apache 2 licensed.
eQTL-analysis-using-ADAM-and-Spark
Analysis of genotypes and gene expression phenotype (eQTLs) using ADAM and Spark
gRPC-maven-helloworld
HelloWorld gRPC using maven
jpdna's Repositories
jpdna/gRPC-maven-helloworld
HelloWorld gRPC using maven
jpdna/eQTL-analysis-using-ADAM-and-Spark
Analysis of genotypes and gene expression phenotype (eQTLs) using ADAM and Spark
jpdna/bam2fastq
Bam to Fastq processing using Toil
jpdna/adam
A genomics processing engine and specialized file format built using Apache Avro, Apache Spark and Parquet. Apache 2 licensed.
jpdna/avocado
A Variant Caller, Distributed. Apache 2 licensed.
jpdna/bcbio-nextgen
Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
jpdna/bdg-convert
Conversions to and from Big Data Genomics Avro Formats. Apache 2 licensed.
jpdna/bdg-convert-ga4gh
Conversions between GA4GH Protobuf and Big Data Genomics Avro Formats. Apache 2 licensed.
jpdna/bdg-formats
Open source formats for scalable genomic processing systems using Avro. Apache 2 licensed.
jpdna/bdghbase
bdghbase: an HBase storage backend for Big Data Genomics
jpdna/cannoli
Big Data Genomics ADAM Pipe API wrappers for bioinformatics tools. Apache 2 licensed.
jpdna/exac_browser
Browser for ExAC consortium data
jpdna/ga4gh-schemas
Work on data models and APIs for Genomic data.
jpdna/GenomicsDB
GenomicsDB
jpdna/GLnexus
Scalable datastore for population genome sequencing, with on-demand joint genotyping
jpdna/glow
An open-source toolkit for large-scale genomic analysis
jpdna/gnomad_browser
tasks for ExAC + gnomad integration pre-ASHG
jpdna/hgvs-eval
automated evaluation suite to assess tools that manipulate HGVS formatted variants
jpdna/mango
A scalable genome browser. Apache 2 licensed.
jpdna/mango-private
mango-private
jpdna/modin
Modin: Speed up your Pandas workflows by changing a single line of code
jpdna/NGS_genotype_calling
jpdna/pb_to_json_test
jpdna/test2
jpdna/test_bdg_kitchen_sink
umbrella bdg project
jpdna/toil-scripts
jpdna/utils
General (non-omics) code used across BDG products. Apache 2 licensed.
jpdna/variant_prioritization
Workflows taking Exome/WGS fastq files to prioritized variants
jpdna/VCFtoFinalReportForBafRegress
Convert a VCF file to the Illumina FinalReport format required as input to the contamination detection tool bafRegress
jpdna/vg
tools for working with variation graphs