Ambarish Kumar's repositories
adam
ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.
archaeopteryx-js
Archaeopteryx.js is a software tool for the visualization and analysis of highly annotated phylogenetic trees.
biocluster
Tutorial on building a computing cluster for bioinformatics
biomarkers
Biomarker collection.
CEVOpen
Contentmining of Open phytochemical literature for medicinal activities
climate
OpenAccess papers mined for Climate Change
CMForestPlots
Things for managing the ContentMine forest plot functionality in normal
cromwell
Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
Data-Science
Repository will contain example code snippet for all most all machine learning algorithms and statistical testing all implemented into Python and R
dplyr
dplyr: A grammar of data manipulation
elife2019
For eLife Sprint 2019
EssOilDB
Restructuring of Essential Oil Database
five-dollar-genome-analysis-pipeline
Workflows used for germline short variant discovery in WGS data
forestplots
forest plots and software to analyse them
galwayecr
Material for invited talk/demo at NUI Galway 2019-04-11
gatk
Official code repository for GATK versions 4 and up
gatk4-jupyter-notebook-tutorials
This repository contains Jupyter Notebooks containing GATK Best Practices Workflows
gatk4-somatic-cnvs
Workflows for somatic copy number variant discovery with GATK4
gatk4-somatic-snvs-indels
Workflows for somatic short variant discovery with GATK4
google-maps-services-python
Python client library for Google Maps API Web Services
haml
HLA Antibody Markup Language - For antibody assay results and expert interpretation
intermine
A powerful open source data warehouse system
MayomicsVC
Variant Calling Pipeline in Cromwell/WDL
neat-genreads
NEAT read simulation tools
openNotebook
Communal methods and links to sub-projects using OpenNotebookScience
optogenetics
AMI tools for searching for optogenetic papers (HT James Sanders)
quantumchem
searching Open Access literature for quantum chemistry (inspiration Leonie Mueck)
simulatedEbolaDataset
Repository contains simulated ebola RNASEQ reads genarated from ebola reference genome with manually called mutations.
SV-Bay
Detection of structural variants in cancer mate-pair and paired-end data
VariantSpark
machine learning for genomic variants