Explore @hammerlab Open Source projects

Hammer Lab (@hammerlab)

hammerlab

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Global Org. Rank 8,841 (Top 3 %)
Registered almost 11 years ago
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Scala
22.4 %

Python
21.2 %

Jupyter Notebook
20.0 %

OCaml
17.6 %

JavaScript
12.9 %

TypeScript
1.2 %

R
1.2 %

TeX
1.2 %

Perl
1.2 %

Shell
1.2 %
Location 🇺🇸 United States
Country Total Rank 4,567
Country Ranking

OCaml
19

Scala
155

Jupyter Notebook
457

TeX
1,781

JavaScript
2,042

Shell
2,709

Perl
3,250

Python
5,500

R
7,261

pileup.js

Interactive in-browser track viewer

grafana-spark-dashboards

Scripts for generating Grafana dashboards for monitoring Spark jobs

spree

Live-updating Spark UI built with Meteor

survivalstan

Library of Stan Models for Survival Analysis

Jupyter Notebook

cytokit

Microscopy Image Cytometry Toolkit

Jupyter Notebook

ppx_deriving_cmdliner

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

flowdec

TensorFlow Deconvolution for Microscopy Data

Jupyter Notebook

guacamole

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

ketrew

Keep Track of Experimental Workflows

yarn-logs-helpers

Scripts for parsing / making sense of yarn logs

genspio

Generate Shell Phrases In OCaml

dask-distributed-on-kubernetes

Deploy dask-distributed on google container engine using kubernetes

Jupyter Notebook

data-canvas

Improved event handling and testing for the HTML5 canvas

cycledash

Variant Caller Analysis Dashboard and Data Management System

prohlatype

Probabilistic HLA typing

kubeface

python parallel map on kubernetes

epidisco

Personalized cancer epitope discovery and peptide vaccine prediction pipeline

sosa

The Sane OCaml String API

biokepi

Bioinformatics Ketrew Pipelines

spark-tests

Utilities for writing tests that use Apache Spark.

t-cell-relation-extraction

Literature mining for T cell relations

Jupyter Notebook

multi-omic-urothelial-anti-pdl1

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

Jupyter Notebook

vcf.js

A VCF parser and variant record model in JavaScript.

magic-rdds

Miscellaneous functionality for manipulating Apache Spark RDDs.

cohorts

Utilities for analyzing mutations and neoepitopes in patient cohorts

spark-bam

Load genomic BAM files using Apache Spark

pygdc

Python API for Genomic Data Commons

concordance

Concordance between variant callers

shapeless-utils

type-classes for structural manipulation of algebraic data types

bai-indexer

Build an index for your BAM Index (BAI)

spark-json-relay

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

coclobas

Configurable Cloudy Batch Scheduler

spark-util

low-level helpers for Apache Spark libraries and tests

t-cell-guide

Human Primary T cells: A Practical Guide

Jupyter Notebook

awesome-clonality

A curated list of awesome clonality and tumor heterogeneity resources

sbt-parent

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

immuno

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

pageant

Parallel Genomic Analysis Toolkit

seltest

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

stanity

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

slim

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

vcf-annotate-polyphen

A tool to annotate human VCF files with PolyPhen2 effect measures

vaf-experiments

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

Jupyter Notebook

style-guides

Guidelines of the Hammer Lab

math-utils

Math and statistics utilities

hlarp

Normalize HLA typing output.

t-cell-data

iterators

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

infino

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

Jupyter Notebook

kerseq

Helpers for sequence prediction with Keras

secotrec

Setup Coclobas/Ketrew Clusters

immune-infiltrate-explorations

Jupyter Notebook

suffix-arrays

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

spark-genomics

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

wobidisco

Workflows Bioinformatics and Discoballs: The Biokepiverse

igv-httpfs

An adaptor which lets IGV talk to HDFS via HttpFS

redaw

Reinvent the Dataset Wheel

melanoma-reanalysis

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

idiogrammatik

An extensible, embeddable karyogram for the browser.

cli-utils

Helpers for creating command-line applications

topeology

Compare neoepitope sequences with epitopes from IEDB

stratotemplate

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

ngsdiagnostics

Diagnostic Scripts for an NGS Pipeline

ogene

Type-safe scripts for genomic file wrangling

bespoke.js

Parsers and fetchers for a cornucopia of bioinformatics formats

mhcflurry-icml-compbio-2016

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

Jupyter Notebook

rinfino

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

coverage-depth

Generate genomic-coverage-depth histograms using Apache Spark

SmartCount

Repository for collaboration on Celldom computer vision solutions

Jupyter Notebook

igvxml

Create IGV session files from the command-line

paper-aocs-chemo-neoantigens

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

Jupyter Notebook

bdgenomics-notebook

flusso

FCS (Flow Cytometry Standard) parser and utility

io-utils

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

variant-calling-benchmarks

Automated and curated variant calling benchmarks for Guacamole

Jupyter Notebook

stratocumulus

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

tcga-blca

Example analysis using Cohorts & TCGA-BLCA data

Jupyter Notebook

cvutils

Computer vision utilities

path-utils

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

discohorts

Generate Cohorts based on Epidisco and/or Biokepi results

spear

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

pysigs

Mutational signature deconvolution onto known signatures

celldom-analysis

Repository for Celldom experiment analysis and configuration

Jupyter Notebook

t-cell-electroporation

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

Jupyter Notebook

genomic-loci

Utilities for representing genomic loci and reference-genomes

stancache

Filecache for stan models

genomic-reads

Library for representing and working with genomic-sequencing reads.

avm

Arteriovenous malformations

epidisco-web

Web interface to easily describe and submit epidisco jobs

nosoi

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

string-utils

String/CSV utilities