Kenneth Daily

Universal Command Line Interface for Amazon Web Services

Analysis of C4 data

Tools for next-generation sequencing in use at the CCR/NCI

AREM -- Aligning Reads by Expectation-Maximization

A template utility for R projects that provides a skeletal project.

An implementation of the Grammar of Graphics in R

Use R Shiny for exploratory analysis of Pathway Commons pathways through R cytoscape.js

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Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations

Harry Mangalam's utilites 'scut' and 'cols'

Directory bookmarks for the shell

Transparent Git Encryption

Tools for the NIH's Helix and Biowulf system

Emacs to Python interface

A Ruffus pipeline for Analysis of High-Throughput Sequencing data

A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and a Genomic Short-read Nucleotide Alignment Program

An R data package for the COSMIC database

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A biplot based on ggplot2

NGS pipelines

Collection of emacs extensions specifically collected for python development, with workflow guidelines!

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Automation for the Sage AWS org-sagebase-sandbox account

The Python developer's guide

GitHub actions to push back to repository eg. updated code

A clean customizable documentation theme for Sphinx

Github Actions for publishing Sphinx HTML output to github pages

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Test out github project automations because I can't use a forked repo to do it.

Landing page for the AWS SDKs on GitHub

A modern, high customizable, responsive Jekyll theme for documention with built-in search.

test out the pr exclusion bot

The official AWS SDK for Java - Version 2

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For the latest version of boto, see https://github.com/boto/boto3 -- Python interface to Amazon Web Services

The low-level, core functionality of boto 3.

Modularized AWS SDK for JavaScript.

Amazon S3 Transfer Manager for Python

AWS SDK for Python

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The official AWS SDK for .NET. For more information on the AWS SDK for .NET, see our web site:

The open source version of the AWS CLI User Guide

User guide for the AWS Cloud Development Kit (CDK).

Clean up stale issues in your repository with GitHub Actions!

CWL interface to the Synapse command line.

testing gh action with versioning

React component based configurations that generate community portals built on top of Synapse

TODO: Move this to ki-tools or Sage

Proof of Concept -- Do Not Use

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Python package for JSON validation by the Sage Bionetworks DCC group

Validate data, metadata, and annotations

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AWS infrastructure for VEO-IBD consortium data management

Validation and processing of GENIE files: https://www.synapse.org/genie

The Synapse Repository Services project is the home of the JSON REST web services for Synapse.

JSON validation schemas

Synapse challenge utility functions

A mosaic detecting software based on phasing and random forest

Code for synchronizing NDAR data with Synapse

An service to auto provision resources on AWS scicomp

GitHub repository for AWS CodeStar Python web service testawsserverless.

A serverless app that periodically polls the public Twitter Standard Search API and invokes a given lambda function to process new tweets

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Score Cell Tracking Results Against Gold Standard NeuroLINCS Data.

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Presentation for U4C

Presentation for May 18, 2015 at OHSU for MEP-LINCS

Presentation about BSMN for Communities group

Presentation at OHSU for LINCS on April 11, 2016

Presentation for Annotations group 2016-05-24

A collection of docker/singularity container build definitions created at UCI U54 Cancer Center for the Cancer Systems Biology Consortium (CSBC) and Physical Sciences in Oncology Network (PS-ON) working group

Template for quickly creating a new Python project and publishing it to PyPI.

Code samples for using Python on Google Cloud Platform

Programmatic interface to Synapse services for Python

JSON schemas for Agora data

Validate BSMN Grant Data

AMP-AD Face To Face presentation on the Wall of Targets

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A Serverless application that runs on AWS Lambda exposing a GraphQL interface for integrating with Synapse

Wellcome Data Re-use Prize: Surveillance

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Basic structure of a R Shiny application for use on Synapse

Collection of Gists

From https://github.com/common-workflow-language/workflows

BSMN common data processing pipeline

An service to auto provision resources on AWS scicomp

personal

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Photography website for dad.

Django coffee site

CfnCluster is a framework that deploys and maintains HPC clusters on AWS.

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code for managing data coordinating operations through Synapse

Moves Synapse files from one bucket to another

Project management code for HBGDki

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This is an example of a workflow that works with the Synapse submission system.

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Template for workshop websites.

Sage Bionetworks derived standards for annotating content in Synapse.

Dash app to show Synapse provenance

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Docker file management

Presentation for HBGDKi Rally 6 kickoff meeting

An R package providing programmatic access to Synapse

Provision a Fedora laptop

Repository with sample code and libraries for obtaining AWS credentials to use with your NIMH Data Archives account

The hackable text editor :atom:

Sage, Synapse and the PCBC

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Bioinformatics containers

Turn (almost) any Python command line program into a full GUI application with one line

Using Git and GitHub with R, Rstudio, and R Markdown

Common compute resources for Sage data scientists

Scripts to migrate data from internal partner sites to public web-site

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R package for systems biology modeling

Interactive Data visualization for PCBC C4 omics data

A repo to collect all materials and resources related to Mozilla Science Lab's Working Open Workshop

Preprocessing and analysis code for MEP-LINCS v1 dataset

PCBC Sample Metadata

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MEMA Preprocessing, QA and Normalizing Functions

Helper Scripts to ease routine synapse python client oriented tasks

Website and materials for Rhody R Stats intro r workshop

Making it easy to talk to GitHub from R

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Shiny application to authenticate synapse users through their session token by reading it with javascript.

Instructor training preparation, September 2015

Easy interactive web applications with R

Presentations for Bozeman 2015

This repository contains Data Carpentry lessons on using spreadsheets for data wrangling.

Tutorial on organizing data in spreadsheets.

AltAnalyze is a multi-functional and easy-to-use software package for begining-to-end genomic analyses.

MEP-LINCS Common Cancer Lines

CloudBioLinux: configure virtual (or real) machines with tools for biological analyses

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Code supporting my U4C Project Submission

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A curated list of awesome R frameworks, packages and software.

Functionality to knit RMarkdown documents to Synapse wiki pages.

R Interface to the jQuery Plug-in DataTables

Weather Underground conditions/forecasts scripts designed for conky integration

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d3 heatmap

Scratch and testing space for Synapse example

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RISmed is an R package for downloading and analyzing data from the NCBI databases

Download content from NCBI databases

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Code for running/loading seq datasets using Synapse.

Swirl courses for Synapse

Making it easier for R to talk to github

Small Vignettes of Synapse use

A comprehensive toolbox for swirl instructors.

A collection of interactive courses for the swirl R package.

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Code for UISO publication

Code that is run by Synapse user PCBCMonitor.

Generating PBC ISA-Tab files

Publication "Assessment of Cancer Cell Line Representativeness using Microarrays for Merkel Cell Carcinoma" to the Journal of Investigative Dermatology

Publication "Assessment of Cancer Cell Line Representativeness using Microarrays for Merkel Cell Carcinoma" to the Journal of Investigative Dermatology

Synodos Data Explorer(SyDE) Shiny App

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Code and reports for PCBC DESeq mRNA differential expression analysis of stem cell lines

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The R programmatic interface to Synapse services

R configurations for Docker

The lecture slides for Coursera's Data Analysis class

Code for the Kyoto Cold Drip Project

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Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms

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This simple one-page website is a way for people to have a very quick and easy personable website that aggregates your activity and positions a simple logo, a portrait and some description text in a nicely-formatted manner. This is licensed under the MIT and GPL licenses.

Jason Bryer's Github projects

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Tools for producing pseudo-cgh of next-generation sequencing data

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Dermatology Branch Journal Club, 2014-01-31

Pieces of reusable code for data analysis

DermJournalClub_20130614

The Leek group guide to data sharing

Dermatology Branch Journal Club Presentation

Gut metagenome in European women with normal, impaired and diabetic glucose control

lumpy: a general probabilistic framework for structural variant discovery

Pluggable rating fields in Django.

Infrastructure code to support DNA pipeline

Git page

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Shell scripts to create basic files and directories for books and other long documents.

PAthway Representation and Analysis by Direct Inference on Graphical Models