CD2H gitForager

Hammer Lab

Login: hammerlab

Company: null

Location: Charleston, SC

email: info@hammerlab.org

Blog: http://hammerlab.org

Members

Repositories

adam: A genomics processing engine and specialized file format built using Apache Avro, Apache Spark and Parquet. Apache 2 licensed.
algebra: Experimental project to lay out basic algebra type classes
args4s: Scala-focused OptionHandlers for args4j
avm: Arteriovenous malformations
avocado: A Variant Caller, Distributed
awesome-clonality: A curated list of awesome clonality and tumor heterogeneity resources
bai-indexer: Build an index for your BAM Index (BAI)
bdgenomics-notebook: null
bdg-formats: null
bdg-utils: General (non-omics) code used across BDG products. Apache 2 licensed.
bespoke.js: Parsers and fetchers for a cornucopia of bioinformatics formats
biocaml: OCaml Bioinformatics Library
biokepi: Bioinformatics Ketrew Pipelines
biopam: OPAM repository for bioinformatics tools.
bowtie: An ultrafast memory-efficient short read aligner
case-app: Type-level & seamless command-line argument parsing for Scala
cli-utils: Helpers for creating command-line applications
cli-utils: Helpers for creating command-line applications
coclobas: Configurable Cloudy Batch Scheduler
codex: Processing worfklows for CODEX cytometric imaging data
cohorts: Utilities for analyzing mutations and neoepitopes in patient cohorts
cohorts-example: Example usage of Cohorts
concordance: Concordance between variant callers
cookiecutter-hammerlab: A cookiecutter template for pip-installable python projects, specific to Hammer lab conventions
coverage-depth: Generate genomic-coverage-depth histograms using Apache Spark
cvutils: Computer vision utilities
cycledash: Variant Caller Analysis Dashboard and Data Management System
cycledash-styleguide: null
dask-distributed-on-kubernetes: Deploy dask-distributed on google container engine using kubernetes
data-canvas: Improved event handling and testing for the HTML5 canvas
dataproc: Simple python script for running a Spark job on an ephemeral Google Cloud dataproc cluster
discohorts: Generate Cohorts based on Epidisco and/or Biokepi results
epidisco: Personalized cancer epitope discovery and peptide vaccine prediction pipeline
epidisco-web: Web interface to easily describe and submit epidisco jobs
filter-bam: Stand-alone utility for filtering a BAM file to specific genomic regions, using Apache Spark.
flowdec: Tensorflow Deconvolution for Microscopy
gdc-helpers: Utilities and tricks to help efficiently download data from GDC (Genomics Data Commons)
genomic-loci: Utilities for representing genomic loci and reference-genomes
genomic-reads: Library for representing and working with genomic-sequencing reads.
genomic-readsets: Library for representing and working with sets of genomic-sequencing reads, e.g. BAM files.
genomic-reference: Utilities for representing and working with reference genomes
genomic-utils: Utilities for working with genomic bases, cigar strings, and phred scores.
genspio: Generate Shell Phrases In OCaml
grafana-spark-dashboards: Scripts for generating Grafana dashboards for monitoring Spark jobs
guacamole: Spark-based variant calling, with experimental support for multi-sample somatic calling (including RNA) and local assembly
Hadoop-BAM: Hadoop-BAM is a Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework
hlarp: Normalize HLA typing output.
icfp2017-papers: Link to preprints for ICFP'17 and colocated events
idiogrammatik: An extensible, embeddable karyogram for the browser.
igv-httpfs: An adaptor which lets IGV talk to HDFS via HttpFS
igvxml: Create IGV session files from the command-line
immune-infiltrate-explorations: null
immuno: Use somatic mutations to choose a personalized cancer vaccine (tumor-specific immunogenic peptides)
immuno_research: Predicting immunogenicity of short peptides
imseq: IMSEQ - IMmunogenetic SEQuence Analysis
inferelator_ng: Inferelator refactor and generalization.
infiltrate-rnaseq-pipeline: null
infino: Infino: a Bayesian hierarchical model improves estimates of immune infiltration into tumor microenvironment
infino-docker: Development environment for infino.
invis: A tool for exploring high-dimensional RNA sequences from in vitro selection
io-utils: Libraries for console/file I/O, processing/formatting sizes in bytes, etc.
iterators: Enrichment-methods for Scala collections (Iterators, Iterables, Arrays)
keredofi: Ketrew-Related DockerFiles (contents of this repo are software-generated)
kerseq: Helpers for sequence prediction with Keras
ketrew: Keep Track of Experimental Workflows
kubeface: python parallel map on kubernetes
magic-rdds: Miscellaneous functionality for manipulating Apache Spark RDDs.
math-utils: Math and statistics utilities
melanoma-reanalysis: Online Materials: Somatic Mutations, Neoepitope Homology and Inflammation in Melanomas Treated with CTLA-4 Blockade
mhcflurry-icml-compbio-2016: Data and analysis notebooks for Predicting Peptide-MHC Binding Affinities With Imputed Training Data
multi-omic-urothelial-anti-pdl1: Contribution of systemic and somatic factors to clinical response and resistance in urothelial cancer: an exploratory multi-omic analysis
ngsdiagnostics: Diagnostic Scripts for an NGS Pipeline
nosoi: Exploration of evolutionary signatures within viral proteomes by making use of MHC binding predictions
ogene: Type-safe scripts for genomic file wrangling
oml: OCaml Math Library
oml: OCaml Math Library
opentrons: Python API for writing protocols and running them on Opentrons robots
pageant: Parallel Genomic Analysis Toolkit
paper-aocs-chemo-neoantigens: Manuscript on chemotherapy-induced neoantigens in samples from the Australian Ovarian Cancer Study
path-utils: Scala convenience-wrapper for java.nio.file.Path
pileup.js: Interactive in-browser track viewer
ppx_deriving_cmdliner: Ppx_deriving plugin for generating command line interfaces from types (Cmdliner.Term.t)
prohlatype: Probabilistic HLA typing
pygdc: Python API for Genomic Data Commons
pysigs: Mutational signature deconvolution onto known signatures
quince: Scalable genome variant analytics using the ADAM project
quinine: A refreshing treatment for all quality control ailments. Apache 2 licensed.
redaw: Reinvent the Dataset Wheel
rinfino: R client to run infino (http://github.com/hammerlab/infino)
sbt-base.g8: giter8 template for hammerlab projects using the hammerlab/sbt-parent `base` plugin
sbt-compat: An sbt plugin that backports parts of sbt 1's public API on top of sbt 0.13 implementation
sbt-dependency-graph: sbt plugin to create a dependency graph for your project
sbt-parent: SBT plugins for publishing to Maven Central, shading and managing dependencies, reporting to Coveralls from TravisCI, and more
sbt-parent.g8: giter8 template for the hammerlab/sbt-parent SBT plugin
scala-parent-pom: POM with miscellaneous boilerplate for Scala 2.11 projects
scikit-bio: scikit-bio is an open-source, BSD-licensed, Python package providing data structures, algorithms, and educational resources for bioinformatics.
secotrec: Setup Coclobas/Ketrew Clusters
seltest: The simple, fast, visual testing framework for web applications.
shapeless-utils: shapeless-style type-classes for structural manipulation of algebraic data types
simplesetup: Routines to simplify setup.py
slim: Node server that listens to Spark events, aggregates statistics, and writes them to Mongo
sosa: The Sane OCaml String API
spark-bam: Load genomic BAM files using Apache Spark
cli-utils: Helpers for creating command-line applications
cli-utils: Helpers for creating command-line applications
spark-genomics: Aggregation of various hammerlab-org genomic, spark, and scala libraries
spark-json-relay: SparkListener that converts SparkListenerEvents to JSON and forwards them to an external service via RPC.
spark-tests: Utilities for writing tests that use Apache Spark.
spark-util: Low-level helpers for Spark libraries and tests
spear: WIP: SparkListener that maintains info about jobs, stages, tasks, executors, and RDDs in MongoDB.
spree: Live-updating Spark UI built with Meteor
stancache: Filecache for stan models
stanity: python convenience functions for working with Stan models (via pystan)
stratocumulus: DEPRECATED: we don't really maintain this any more, we use Coclobas:
stratotemplate: DEPRECATED: we don't really maintain this any more, we use Coclobas:
string-utils: String/CSV utilities
style-guides: Guidelines of the Hammer Lab
suffix-arrays: Spark-based implementation of pDC3, a linear-time parallel suffix-array-construction algorithm
survivalstan: Library of Stan Models for Survival Analysis
t-cell-guide: Human Primary T cells: A Practical Guide
tcga-blca: Example analysis using Cohorts & TCGA-BLCA data
test-utils: Unit-testing utilities
topeology: Compare neoepitope sequences with epitopes from IEDB
typechecks: Type checking helpers for Python
typechecks: Type checking helpers for Python
vaf-experiments: A step-by-step guide to estimate tumor clonality/purity from variant allele frequency data
variant-calling-benchmarks: Automated and curated variant calling benchmarks for Guacamole
vcf-annotate-polyphen: A tool to annotate human VCF files with PolyPhen2 effect measures
vcf.js: A VCF parser and variant record model in JavaScript.
wobidisco: Workflows Bioinformatics and Discoballs: The Biokepiverse
yarn-logs-helpers: Scripts for parsing / making sense of yarn logs

This work is supported by the National Institutes of Health's National Center for Advancing Translational Sciences, Grant Number U24TR002306. This work is solely the responsibility of the creators and does not necessarily represent the official views of the National Institutes of Health.