Projects in Awesome Lists by hammerlab
A curated list of projects in awesome lists by hammerlab .
https://github.com/hammerlab/grafana-spark-dashboards
Scripts for generating Grafana dashboards for monitoring Spark jobs
Last synced: 26 Apr 2025
https://github.com/hammerlab/spree
Live-updating Spark UI built with Meteor
Last synced: 26 Apr 2025
https://github.com/hammerlab/survivalstan
Library of Stan Models for Survival Analysis
Last synced: 05 May 2025
https://github.com/hammerlab/ppx_deriving_cmdliner
Ppx_deriving plugin for generating command line interfaces from types (Cmdliner.Term.t)
cli command-line-parser ocaml ppx ppx-extension
Last synced: 26 Apr 2025
https://github.com/hammerlab/flowdec
TensorFlow Deconvolution for Microscopy Data
Last synced: 18 Mar 2026
https://github.com/hammerlab/guacamole
Spark-based variant calling, with experimental support for multi-sample somatic calling (including RNA) and local assembly
Last synced: 26 Apr 2025
https://github.com/hammerlab/yarn-logs-helpers
Scripts for parsing / making sense of yarn logs
Last synced: 14 Oct 2025
https://github.com/hammerlab/genspio
Generate Shell Phrases In OCaml
edsl hacktoberfest ocaml posix shell
Last synced: 26 Apr 2025
https://github.com/hammerlab/dask-distributed-on-kubernetes
Deploy dask-distributed on google container engine using kubernetes
Last synced: 12 Jun 2025
https://github.com/hammerlab/data-canvas
Improved event handling and testing for the HTML5 canvas
Last synced: 28 Jul 2025
https://github.com/hammerlab/cycledash
Variant Caller Analysis Dashboard and Data Management System
Last synced: 26 Apr 2025
https://github.com/hammerlab/epidisco
Personalized cancer epitope discovery and peptide vaccine prediction pipeline
biokepi epitope-discovery ocaml pipeline
Last synced: 26 Apr 2025
https://github.com/hammerlab/biokepi
Bioinformatics Ketrew Pipelines
bioinformatics-ketrew-pipelines bioinformatics-pipeline ketrew ocaml
Last synced: 06 Sep 2025
https://github.com/hammerlab/spark-tests
Utilities for writing tests that use Apache Spark.
Last synced: 26 Apr 2025
https://github.com/hammerlab/t-cell-relation-extraction
Literature mining for T cell relations
Last synced: 08 Sep 2025
https://github.com/hammerlab/magic-rdds
Miscellaneous functionality for manipulating Apache Spark RDDs.
Last synced: 26 Apr 2025
https://github.com/hammerlab/multi-omic-urothelial-anti-pdl1
Contribution of systemic and somatic factors to clinical response and resistance in urothelial cancer: an exploratory multi-omic analysis
Last synced: 08 Jul 2025
https://github.com/hammerlab/vcf.js
A VCF parser and variant record model in JavaScript.
Last synced: 26 Apr 2025
https://github.com/hammerlab/spark-bam
Load genomic BAM files using Apache Spark
Last synced: 26 Apr 2025
https://github.com/hammerlab/cohorts
Utilities for analyzing mutations and neoepitopes in patient cohorts
Last synced: 26 Apr 2025
https://github.com/hammerlab/shapeless-utils
type-classes for structural manipulation of algebraic data types
Last synced: 26 Apr 2025
https://github.com/hammerlab/concordance
Concordance between variant callers
Last synced: 24 Jan 2026
https://github.com/hammerlab/spark-json-relay
SparkListener that converts SparkListenerEvents to JSON and forwards them to an external service via RPC.
Last synced: 05 Oct 2025
https://github.com/hammerlab/bai-indexer
Build an index for your BAM Index (BAI)
Last synced: 26 Apr 2025
https://github.com/hammerlab/spark-util
low-level helpers for Apache Spark libraries and tests
Last synced: 29 Oct 2025
https://github.com/hammerlab/awesome-clonality
A curated list of awesome clonality and tumor heterogeneity resources
Last synced: 28 Feb 2026
https://github.com/hammerlab/immuno
Use somatic mutations to choose a personalized cancer vaccine (tumor-specific immunogenic peptides)
Last synced: 26 Apr 2025
https://github.com/hammerlab/t-cell-guide
Human Primary T cells: A Practical Guide
Last synced: 26 Apr 2025
https://github.com/hammerlab/sbt-parent
SBT plugins for publishing to Maven Central, shading and managing dependencies, reporting to Coveralls from TravisCI, and more
Last synced: 26 Apr 2025
https://github.com/hammerlab/stanity
python convenience functions for working with Stan models (via pystan)
Last synced: 26 Apr 2025
https://github.com/hammerlab/seltest
The simple, fast, visual testing framework for web applications.
Last synced: 26 Apr 2025
https://github.com/hammerlab/vcf-annotate-polyphen
A tool to annotate human VCF files with PolyPhen2 effect measures
Last synced: 13 Jul 2025
https://github.com/hammerlab/slim
Node server that listens to Spark events, aggregates statistics, and writes them to Mongo
Last synced: 26 Apr 2025
https://github.com/hammerlab/vaf-experiments
A step-by-step guide to estimate tumor clonality/purity from variant allele frequency data
Last synced: 06 Sep 2025
https://github.com/hammerlab/infino
Infino: a Bayesian hierarchical model improves estimates of immune infiltration into tumor microenvironment
Last synced: 26 Apr 2025
https://github.com/hammerlab/iterators
Enrichment-methods for Scala collections (Iterators, Iterables, Arrays)
Last synced: 15 Jul 2025
https://github.com/hammerlab/igv-httpfs
An adaptor which lets IGV talk to HDFS via HttpFS
Last synced: 26 Apr 2025
https://github.com/hammerlab/wobidisco
Workflows Bioinformatics and Discoballs: The Biokepiverse
Last synced: 08 Oct 2025
https://github.com/hammerlab/suffix-arrays
Spark-based implementation of pDC3, a linear-time parallel suffix-array-construction algorithm
Last synced: 31 Jul 2025
https://github.com/hammerlab/spark-genomics
Aggregation of various hammerlab-org genomic, spark, and scala libraries
Last synced: 26 Apr 2025
https://github.com/hammerlab/kerseq
Helpers for sequence prediction with Keras
Last synced: 26 Apr 2025
https://github.com/hammerlab/idiogrammatik
An extensible, embeddable karyogram for the browser.
Last synced: 10 Mar 2026
https://github.com/hammerlab/melanoma-reanalysis
Online Materials: Somatic Mutations, Neoepitope Homology and Inflammation in Melanomas Treated with CTLA-4 Blockade
Last synced: 02 Feb 2026
https://github.com/hammerlab/topeology
Compare neoepitope sequences with epitopes from IEDB
Last synced: 09 Mar 2026
https://github.com/hammerlab/cli-utils
Helpers for creating command-line applications
Last synced: 17 Aug 2025
https://github.com/hammerlab/ogene
Type-safe scripts for genomic file wrangling
Last synced: 09 Sep 2025
https://github.com/hammerlab/stratotemplate
DEPRECATED: we don't really maintain this any more, we use Coclobas:
Last synced: 17 May 2026
https://github.com/hammerlab/mhcflurry-icml-compbio-2016
Data and analysis notebooks for Predicting Peptide-MHC Binding Affinities With Imputed Training Data
Last synced: 26 Apr 2025
https://github.com/hammerlab/ngsdiagnostics
Diagnostic Scripts for an NGS Pipeline
Last synced: 26 Feb 2025
https://github.com/hammerlab/bespoke.js
Parsers and fetchers for a cornucopia of bioinformatics formats
Last synced: 06 Aug 2025
https://github.com/hammerlab/io-utils
Libraries for console/file I/O, processing/formatting sizes in bytes, etc.
Last synced: 13 May 2026
https://github.com/hammerlab/tcga-blca
Example analysis using Cohorts & TCGA-BLCA data
Last synced: 20 Nov 2025
https://github.com/hammerlab/variant-calling-benchmarks
Automated and curated variant calling benchmarks for Guacamole
Last synced: 26 Feb 2025
https://github.com/hammerlab/paper-aocs-chemo-neoantigens
Manuscript on chemotherapy-induced neoantigens in samples from the Australian Ovarian Cancer Study
Last synced: 28 Jul 2025
https://github.com/hammerlab/flusso
FCS (Flow Cytometry Standard) parser and utility
Last synced: 26 Feb 2025
https://github.com/hammerlab/path-utils
Scala convenience-wrapper for java.nio.file.Path
Last synced: 05 Oct 2025
https://github.com/hammerlab/igvxml
Create IGV session files from the command-line
Last synced: 21 Jun 2025
https://github.com/hammerlab/rinfino
R client to run infino (http://github.com/hammerlab/infino)
Last synced: 18 Oct 2025
https://github.com/hammerlab/coverage-depth
Generate genomic-coverage-depth histograms using Apache Spark
Last synced: 15 May 2026
https://github.com/hammerlab/smartcount
Repository for collaboration on Celldom computer vision solutions
Last synced: 11 Jan 2026
https://github.com/hammerlab/stratocumulus
DEPRECATED: we don't really maintain this any more, we use Coclobas:
Last synced: 16 Apr 2026
https://github.com/hammerlab/nosoi
Exploration of evolutionary signatures within viral proteomes by making use of MHC binding predictions
Last synced: 20 Aug 2025
https://github.com/hammerlab/epidisco-web
Web interface to easily describe and submit epidisco jobs
Last synced: 26 Feb 2025
https://github.com/hammerlab/discohorts
Generate Cohorts based on Epidisco and/or Biokepi results
Last synced: 18 Jun 2025
https://github.com/hammerlab/pysigs
Mutational signature deconvolution onto known signatures
Last synced: 26 Feb 2025
https://github.com/hammerlab/stancache
Filecache for stan models
filecache mcmc reproducible-research stan-model
Last synced: 26 Feb 2025
https://github.com/hammerlab/genomic-reads
Library for representing and working with genomic-sequencing reads.
Last synced: 15 May 2026
https://github.com/hammerlab/genomic-loci
Utilities for representing genomic loci and reference-genomes
Last synced: 10 May 2026
https://github.com/hammerlab/celldom-analysis
Repository for Celldom experiment analysis and configuration
Last synced: 18 Nov 2025
https://github.com/hammerlab/spear
WIP: SparkListener that maintains info about jobs, stages, tasks, executors, and RDDs in MongoDB.
Last synced: 13 May 2026
https://github.com/hammerlab/t-cell-electroporation
Code/Data repository for "Electroporation characteristics of human primary T cells"
Last synced: 20 Nov 2025
https://github.com/hammerlab/gdc-helpers
Utilities and tricks to help efficiently download data from GDC (Genomics Data Commons)
Last synced: 22 Jul 2025
https://github.com/hammerlab/genomic-readsets
Library for representing and working with sets of genomic-sequencing reads, e.g. BAM files.
Last synced: 28 Oct 2025
https://github.com/hammerlab/keredofi
Ketrew-Related DockerFiles (contents of this repo are software-generated)
Last synced: 03 Mar 2026
https://github.com/hammerlab/sbt-base.g8
giter8 template for hammerlab projects using the hammerlab/sbt-parent `base` plugin
Last synced: 10 Oct 2025
https://github.com/hammerlab/scala-parent-pom
POM with miscellaneous boilerplate for Scala 2.11 projects
Last synced: 02 Mar 2026
https://github.com/hammerlab/infino-docker
Development environment for infino.
Last synced: 11 Jul 2025
https://github.com/hammerlab/genomic-utils
Utilities for working with genomic bases, cigar strings, and phred scores.
Last synced: 12 May 2026