Ryan Williams

Login: ryan-williams

Company: Hammer Lab @ Mt. Sinai

Location: New York

Bio: null

Blog:

Blog:

Member of

1. Hammer Lab

Repositories

adam

Fork of ADAM, used to pick up various patches before they're released

adam-helpers

Scripts for fetching and caching ADAM builds, by version number or git SHA.

anchor-voronoi

Some hacks toward clicking links on webpages with minimal effort.

arduino

a place for my arduino hacks

args4s

Scala-focused OptionHandlers for args4j

bdg-formats

Open source formats for scalable genomic processing systems using Avro. Apache 2 licensed.

bdg-utils

General (non-omics) code used across BDG products. Apache 2 licensed.

bedtools2

A powerful toolset for genome arithmetic.

BezierInfo-2

A from-the-ground-up rewrite of https://pomax.github.io/bezierinfo, using react, babel, webpack, and other modern things.

bids

Rent bids for Evan's house

carbon

Carbon is one of the components of Graphite, and is responsible for receiving metrics over the network and writing them down to disk using a storage backend.

case-app

Type-level & seamless command-line argument parsing for Scala

cats

Lightweight, modular, and extensible library for functional programming.

cloudinary_scala

Cloudinary Scala Client Library

collectd

The system statistics collection daemon. Mirror of the canonical repository (updated automatically). Please send Pull Requests here!

commons

Twitter common libraries for python and the JVM

coverage-depth

Generate genomic-coverage-depth histograms using Apache Spark

coverage-test

Test Coveralls+Maven+Scala project

cyanite

cassandra backed carbon daemon and metric web service

dashboard

null

daviddudson.github.io

Personal website/blog etc.

dillinger

The last Markdown editor, ever.

eggo

Ready-to-go Parquet-formatted public 'omics datasets

filter-bam

Stand-alone utility for filtering a BAM file to specific genomic regions, using Apache Spark.

fm-index-v2

A fork of Ferragina and Venturini's "FM Index v2"

freebayes

Bayesian haplotype-based polymorphism discovery and genotyping.

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.

git-commit-notifier

Sends HTML email commit messages splitting commits that were pushed in one step. Changes are highlighted per word.

git-helpers

A few helpers for augmenting and prettifying existing git functionality.

grafana

Grafana - A Graphite & InfluxDB Dashboard and Graph Editor

graphite-api

Graphite-web, without the interface. Just the rendering HTTP API.

graphite-web

A highly scalable real-time graphing system

graphs

Playground for interactive JS-based graph viz

guacamole

simple Spark-based variant calling

Hadoop-BAM

Hadoop-BAM is a Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework with the Picard SAM JDK, and command line tools similar to SAMtools.

hilbert

code for generating hilber-curve-color-picker images

hilbert-js

Node library for working with 2-d and 3-d Hilbert curves.

homebrew

The missing package manager for OS X.

htsjdk

A Java API for high-throughput sequencing data (HTS) formats.

intellij-logs

Dump of IntelliJ IDEA logs, for linking to from youtrack issues

io-utils

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

iterator

Some Scala Iterators and useful Iterator-related abstractions

jekyll-table-of-contents

A simple JavaScript table of contents, designed for Jekyll (or similar) sites.

jss

JSON processing command line tool based on JSONSelect (CSS-like selectors for JSON)

jupyter-nodejs

A node.js kernel for jupyter/ipython

level-tsd

null

lightning-hexbin

React-based canvas hexbin implementation

ls-helpers

null

lunch-and-learns

Slides from my hammerlab Lunch-and-Learns

magic-rdds

Miscellaneous functionality for manipulating Apache Spark RDDs.

math-utils

Math and statistics utilities

maven-sbt-ivy-resolution

Example of differing ivy resolution between Maven and SBT

meteor-test

Simple repo for testing MeteorJS page-refresh rate

mill

Your shiny new Scala build tool!

mvn2pants

Scripts used by Square to convert Maven pom.xml files to BUILD files

node-array-utils

Some array utilities for node.js

node-utils

Some node.js helpers

oboe-test

Test code related to https://github.com/jimhigson/oboe.js/issues/44

ocaml-from-the-very-beginning

exercises from working through "OCaml from the Very Beginning"

pageant

Parallel Genomic Analysis Toolkit

paradise

DEPRECATED - experimental macro annotations

paths

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

pileup.js

Interactive in-browser track viewer

polar

Some code and LaTeX related to comparing polar and rectangular coordinate systems.

proposals-2017

null

quinine

A refreshing treatment for all quality control ailments. Apache 2 licensed.

Risk

An odds calculator for the board game Risk

samtools-helpers

A few helper scripts for working with samtools

sbt-compat

An sbt plugin that backports parts of sbt 1's public API on top of sbt 0.13 implementation

sbt-coveralls

Sbt plugin for uploading Scala code coverage to coveralls

sbt-microsites

An sbt plugin to create awesome microsites for your project

sbt-parent

SBT plugin factoring out boilerplate for publishing to Maven Central and optionally cross-building against Apache Spark 1.x and 2.x versions.

sbt-scoverage

sbt plugin for scoverage

sbt-sonatype

A sbt plugin for publishing Scala/Java projects to the Maven central.

scala

The Scala programming language

scala-bugs

Repros of scala/sbt bugs that I run in to

scala.github.com

The Scala Documentation website

scalajs-spa-tutorial

Tutorial for creating a simple Single Page Application in ScalaJS

scala-pkg-deps

Hacky tool for inferring Scala projects' intra-project, inter-package dependencies and rendering them to DOT graphs.

screen-helpers

Some useful scripts for using `screen`

shapeless-utils

shapeless-style type-classes for structural manipulation of algebraic data types

sigma.js

A JavaScript library dedicated to graph drawing

slate

A window management application (replacement for Divvy/SizeUp/ShiftIt)

slate-files

My config files for the Slate window manager: https://github.com/jigish/slate

spark

Mirror of Apache Spark

spark-bam

Extension of HadoopGenomics/hadoop-bam

spark-bugs

Dumping ground for repros of issues with Apache Spark

spark-commands

Interfaces for creating CLI-runnable and testable Spark commands/apps

spark-helpers

Scripts for fetching and caching Spark builds, by version number or git SHA.

spark-tests

Utilities for writing tests that use Apache Spark.

spark-util

Low-level helpers for Spark libraries and tests

spire

Powerful new number types and numeric abstractions for Scala.

splash-2017

Slides for SPLASH 2017 talk: "Genomic Data Analysis in Scala" https://conf.researchr.org/track/scala-2017/scala-2017-papers#program

stack-traces

Utility for parsing Java stack traces

streaming-wc-l

A line-count utility that outputs intermediate counts in a variety of configurable ways

string-utils

String/CSV utilities

suffix-arrays

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

test-sbt

Tests of SBT configurations

test-utils

Unit-testing utilities

trajectories

Simulations of parabolic trajectories

tut

doc/tutorial generator for scala

variant-calling-benchmarks

Automated and curated variant calling benchmarks for Guacamole

vg

tools for working with variant graphs

viz

Toy javascript algorithm visualizations

webdiff

Two-column web-based git difftool

website

The source for scala-sbt.org

webtreemap

web-based treemap

whiskeyoclock

null

whisper

Whisper is a file-based time-series database format for Graphite.

Commits To