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adam

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

adam-fx

An ADAM extension library for loading .vcf files annotated with SnpEff and SnpSift.

atac-seq-pipeline

ENCODE ATAC-seq pipeline

avocado

A Variant Caller, Distributed. Apache 2 licensed.

avocado-1

Avocado is a multi-scale deep tensor factorization model that learns a latent representation of the human epigenome and enables imputation of epigenomic experiments that have not yet been performed.

bam.iobio.io

http://bam.iobio.io

bdg-convert

Conversions to and from Big Data Genomics Avro Formats. Apache 2 licensed.

bdg-formats

Open source formats for scalable genomic processing systems using Avro. Apache 2 licensed.

bioconda-recipes

Conda recipes for the bioconda channel.

cannoli

Big Data Genomics ADAM Pipe API wrappers for bioinformatics tools. Apache 2 licensed.

cbas

Code for the ICML 2019 paper 'Conditioning by adaptive sampling for robust design'

ccbskillssem.github.io

CompBio Skills Seminar

cgcloud

Image and VM management for Jenkins, Spark and Mesos clusters in EC2

cgl-docker-lib

chipper

Fast proteasomal cleavage detection. Apache-licensed.

ckm

Convolutional Kernel Machines

compbio_seminar_2020

Building reproducible software packages with Python, pip, and conda

dash-bio

Open-source bioinformatics components for Dash

dash-bio-docs-files

Raw files for use in the Dash Bio documentation.

dash-docs

:book: The Official Dash Userguide & Documentation

dash-sample-apps

Open-source demos hosted on Dash Gallery

deseq2

Differential gene expression analysis based on the negative binomial distribution

empowherment

empowherment2

endive

epitome

Pipeline for predicting ChIP-seq peaks in novel cell types using chromatin accessibility

ervmap

ERVmap is one part curated database of human proviral ERV loci and one part a stringent algorithm to determine which ERVs are transcribed in their RNA seq data.

fig

A tool for Finding Interesting variants that modify regulatory Grammar.

ga4gh-schemas

Models and APIs for Genomic data. RETIRED 2018-01-24