Discover hammerlab/genomic-loci Open Source project

Scripts for generating Grafana dashboards for monitoring Spark jobs

276

grafana-spark-dashboards

Live-updating Spark UI built with Meteor

241

spree

Library of Stan Models for Survival Analysis

189

survivalstan

Microscopy Image Cytometry Toolkit

123

cytokit

Ppx_deriving plugin for generating command line interfaces from types (Cmdliner.Term.t)

115

ppx_deriving_cmdliner

TensorFlow Deconvolution for Microscopy Data

flowdec

Spark-based variant calling, with experimental support for multi-sample somatic calling (including RNA) and local assembly

guacamole

Keep Track of Experimental Workflows

ketrew

Scripts for parsing / making sense of yarn logs

yarn-logs-helpers

Shell

genspio

Generate Shell Phrases In OCaml

Deploy dask-distributed on google container engine using kubernetes

dask-distributed-on-kubernetes

Improved event handling and testing for the HTML5 canvas

data-canvas

Variant Caller Analysis Dashboard and Data Management System

cycledash

prohlatype

Probabilistic HLA typing

python parallel map on kubernetes

kubeface

Personalized cancer epitope discovery and peptide vaccine prediction pipeline

epidisco

The Sane OCaml String API

sosa

Bioinformatics Ketrew Pipelines

biokepi

Utilities for writing tests that use Apache Spark.

spark-tests

Literature mining for T cell relations

t-cell-relation-extraction

Contribution of systemic and somatic factors to clinical response and resistance in urothelial cancer: an exploratory multi-omic analysis

multi-omic-urothelial-anti-pdl1

A VCF parser and variant record model in JavaScript.

vcf.js

Miscellaneous functionality for manipulating Apache Spark RDDs.

magic-rdds

Utilities for analyzing mutations and neoepitopes in patient cohorts

cohorts

Load genomic BAM files using Apache Spark

spark-bam

Python API for Genomic Data Commons

pygdc

Concordance between variant callers

concordance

type-classes for structural manipulation of algebraic data types

shapeless-utils

Build an index for your BAM Index (BAI)

bai-indexer

SparkListener that converts SparkListenerEvents to JSON and forwards them to an external service via RPC.

spark-json-relay

Configurable Cloudy Batch Scheduler

coclobas

low-level helpers for Apache Spark libraries and tests

spark-util

Human Primary T cells: A Practical Guide

t-cell-guide

A curated list of awesome clonality and tumor heterogeneity resources

awesome-clonality

sbt-parent

SBT plugins for publishing to Maven Central, shading and managing dependencies, reporting to Coveralls from TravisCI, and more

Use somatic mutations to choose a personalized cancer vaccine (tumor-specific immunogenic peptides)

immuno

Parallel Genomic Analysis Toolkit

pageant

seltest

The simple, fast, visual testing framework for web applications.

python convenience functions for working with Stan models (via pystan)

stanity

Node server that listens to Spark events, aggregates statistics, and writes them to Mongo

slim

A tool to annotate human VCF files with PolyPhen2 effect measures

vcf-annotate-polyphen

A step-by-step guide to estimate tumor clonality/purity from variant allele frequency data

vaf-experiments

Guidelines of the Hammer Lab

style-guides

math-utils

Math and statistics utilities

Normalize HLA typing output.

hlarp

Enrichment-methods for Scala collections (Iterators, Iterables, Arrays)

t-cell-data

TeX

iterators

Infino: a Bayesian hierarchical model improves estimates of immune infiltration into tumor microenvironment

infino

Helpers for sequence prediction with Keras

kerseq

Setup Coclobas/Ketrew Clusters

secotrec

immune-infiltrate-explorations

Spark-based implementation of pDC3, a linear-time parallel suffix-array-construction algorithm

suffix-arrays

TypeScript

spark-genomics

Aggregation of various hammerlab-org genomic, spark, and scala libraries

Workflows Bioinformatics and Discoballs: The Biokepiverse

wobidisco

igv-httpfs

An adaptor which lets IGV talk to HDFS via HttpFS

Reinvent the Dataset Wheel

redaw

Online Materials: Somatic Mutations, Neoepitope Homology and Inflammation in Melanomas Treated with CTLA-4 Blockade

melanoma-reanalysis

idiogrammatik

An extensible, embeddable karyogram for the browser.

Helpers for creating command-line applications

cli-utils

Compare neoepitope sequences with epitopes from IEDB

topeology

DEPRECATED: we don't really maintain this any more, we use Coclobas:

stratotemplate

Diagnostic Scripts for an NGS Pipeline

ngsdiagnostics

Type-safe scripts for genomic file wrangling

ogene

Parsers and fetchers for a cornucopia of bioinformatics formats

bespoke.js

Data and analysis notebooks for Predicting Peptide-MHC Binding Affinities With Imputed Training Data

mhcflurry-icml-compbio-2016

R client to run infino (http://github.com/hammerlab/infino)

rinfino

coverage-depth

Generate genomic-coverage-depth histograms using Apache Spark

Repository for collaboration on Celldom computer vision solutions

SmartCount

Create IGV session files from the command-line

igvxml

Manuscript on chemotherapy-induced neoantigens in samples from the Australian Ovarian Cancer Study

paper-aocs-chemo-neoantigens

FCS (Flow Cytometry Standard) parser and utility

bdgenomics-notebook

flusso

Libraries for console/file I/O, processing/formatting sizes in bytes, etc.

io-utils

Automated and curated variant calling benchmarks for Guacamole

variant-calling-benchmarks

DEPRECATED: we don't really maintain this any more, we use Coclobas:

stratocumulus

Example analysis using Cohorts & TCGA-BLCA data

tcga-blca

Computer vision utilities

cvutils

Scala convenience-wrapper for java.nio.file.Path

path-utils

Generate Cohorts based on Epidisco and/or Biokepi results

discohorts

WIP: SparkListener that maintains info about jobs, stages, tasks, executors, and RDDs in MongoDB.

spear

Mutational signature deconvolution onto known signatures

pysigs

Repository for Celldom experiment analysis and configuration

celldom-analysis

Code/Data repository for "Electroporation characteristics of human primary T cells"

t-cell-electroporation

Filecache for stan models

stancache

Library for representing and working with genomic-sequencing reads.

genomic-reads

Arteriovenous malformations

avm

Web interface to easily describe and submit epidisco jobs

epidisco-web

Exploration of evolutionary signatures within viral proteomes by making use of MHC binding predictions

nosoi

Perl

string-utils

String/CSV utilities