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Sean Davis

Login: seandavi

Company: National Cancer Institute, National Institutes of Health

Location: Bethesda, MD, 20892, USA

Bio: - Pediatric oncologist - Cancer researcher - Data scientist - Community organizer

Blog:

Member of

Repositories

2016-04-27-NIH: null
adv-r: Advanced R programming: a book
annotation-pipeline: null
ansible-playbooks: Miscellaneous ansible playbooks
asthma: RNA-seq quantifications: gene expression responses to human rhinovirus infection for 6 asthmatic and 6 non-asthmatic donors (SRP046226)
awesome-blogdown: An awesome curated list of blogs built using blogdown
awesome-cancer-variant-databases: A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.
awesome-deepbio: A curated list of awesome deep learning applications in the field of computational biology
awesome-microbes: null
awesome-pipeline: A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin
awesome-single-cell: List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc.
awesome-variant-databases: A collection of genomic variant databases
aws-big-data-blog: null
aws.ec2: AWS EC2 Client Package
aws-glue-samples: AWS Glue code samples
aws.s3: Amazon Simple Storage Service (S3) API Client
aws-services-examples: null
b2_modules: null
basic_gce: null
bio2rdf-scripts: Scripts that Bio2RDF users have created to generate RDF versions of scientific datasets
bioc2016eda: null
Bioc2017BigDataWorkshopSession: Tutorial for working with cloud infrastructure and AWS from R
BioC2018: BioC 2018: Where Software and Biology Connect
BiocAnno2016: null
BiocBrazil2014: Code and vignettes in support of the SummerX Bioconductor course in Brazil
BiocExptDataPkgManuscript: Manuscript describing the Bioconductor ExperimentData package ecosystem
BiocFileCache: Manage Files Across Sessions
BiocGadgets: null
BiocIntegrativeCancerVis: null
BiocIntro: Course material for introductory R / Bioconductor courses
biocMultiAssay: R package(s) demonstrating management of multiassay data on a set of samples
BiocParallel: Bioconductor facilities for parallel evaluation (experimental)
BiocPkgTools: Access Bioconductor repository and project metadata from within R
BiocPoster: null
bioDockerCollection: null
breakdancer: SV detection from paired end reads mapping
bumphunter: bumphunter
CCR_NGS: Tools for next-generation sequencing in use at the CCR/NCI
CCRRNABio2017Abstract: null
CCR-shRNA-browser: null
CGC: null
cgcR: scratch repository for creating and sharing
ChimpHumanBrainData: R data package containing chimp and human brain data .cel files
ci4cc-informatics-resources: Community-maintained list of resources that the CI4CC organization and the larger cancer informatics community have found useful or are developing.
CleversafeTesting: null
ClinicalTrialsAPI: Access the NIH ClinicalTrials.gov REST API
CloudRNAPoster: null
CloudScripts: Miscellaneous scripts for dealing with cloud compute infrastructure
CompleteGenomicsTools: Software for manipulating and visualizing Complete Genomics data, with a focus on cancer
ComplexPhenotypes: null
conference-videos: List of conferences with talk videos posted online
conveyor: NGS pipelines
COSMIC.build57: An R data package for the COSMIC database
cromwell-1: Workflow Execution Engine using WDL
cruzdb: python access to UCSC genomes database
curatedMetagenomicDataHighLoad: null
d3: A JavaScript visualization library for HTML and SVG.
dbGaPDataUse: Access dbGaP study data use and download stats from R
deep-learning-keras-tensorflow: Introduction to Deep Neural Networks with Keras and Tensorflow
Dockerfiles: null
dockerflow: Dockerflow is a workflow runner that uses Dataflow to run a series of tasks in Docker with the Pipelines API
docker_scidb: Dockerize SciDB
DogOsteoVis: null
dotfiles: My dotfiles
driver: Google Drive API client library in R
DSNotes: Random data science and engineering notes
effects: prioritize effects of variant annotations from VEP, SnpEFF, et al.
elk-docker: Elasticsearch, Logstash, Kibana (ELK) Docker image
.emacs.d: null
emacs-d: My .emacs.d directory
emacs-for-python: Collection of emacs extensions specifically collected for python development, with workflow guidelines!
emr-bootstrap-actions: This repository hold the Amazon Elastic MapReduce sample bootstrap actions
F1000R_BiocWorkflows: Project for publishing from Bioconductor to F1000R and back
Flask-Graphene-SQLAlchemy: A demo project for Flask + GraphQL (With Graphene & SQLAlchemy)
genetrack-central: GeneTrack is a genomic data visualization software
GEOmetadb: Github mirror of the GEOmetadb bioconductor package
GEOquery: The bridge between the NCBI Gene Expression Omnibus and Bioconductor
GFFutils: Convert, explore, and manipulate GFF and GTF files (used in bioinformatics) using a sqlite-based approach
gi2017software: Software from GI2017
gitinspector: Automatically exported from code.google.com/p/gitinspector
git-wiki: A quick & dirty git-powered Sinatra wiki
globusT: Globus transfer tool
googleCloudStorageR: Google Cloud Storage API to R
googleComputeEngineR: An R interface to the Google Cloud Compute API, for launching virtual machines
goSTAG: The goSTAG Bioconductor Package
HarvardExtremeComputing: Materials for the Fall 2015 Harvard Extreme Computing course
Helix: Tools for the NIH's Helix and Biowulf system
HiClink: HiClink: a scalable, flexible, robust framework for HiC data
HiCUtils: null
homebrew: The missing package manager for OS X.
hour_of_code: Materials for Hour of Code using R
HumanDiseaseOntology: Repository for the Human Disease Ontology.
hyde: A brazen two-column theme for Jekyll.
Illumina27kMethylationTitration: null
Illumina450kMethylationTitration: null
InteractiveApps_Bioc2017: null
IntroToBiocAnno: null
irods_contrib: A pooled collection of community-contributed code that works alongside iRODS
iRODS-NCI: null
ITR: null
jbrowse: AJAX Genome Browser
jekyll-rstudio-demo: Jekyll + knitr + htmlwidgets + citations = publish science from RStudio
jheatmap: Javascript Heatmap viewer
knitr-jekyll: Automatically knit R Markdown documents, build them with Jekyll, and serve the website with servr locally
labs: Rmd source files for the HarvardX series PH525x
LearnBioconductor: Training material for a Fall, 2014 introductory R / Bioconductor course
lofreq: LoFreq Star: Sensitive variant calling from sequencing data
logstash_play: null
MachineLearningIntro: Machine learning use cases for teaching
Mammomics: Mammomics project web app and site
medic: a command-line tool to maintain a DB mirror of MEDLINE
methylumi: null
MultiplatformGEOSurvey: A short use case for GEOmetadb and dplyr
MutationTools: null
MyNotes: null
mysql2postgres: Mysqldump, writing in postgresql format
MysterySamples: null
NCI60_SuperLearner: Code and data for running the super learner with the NCI60 human tumor cell lines
NewPkg: null
nextflow-rnastar: nextflow pipeline for transcriptome quantificaton using STAR and featurecounts
ngCGH: Tools for producing pseudo-cgh of next-generation sequencing data
ngs: Next Gen Sequencing Utilities
ngs-1: NGS Language Bindings
ngs-analysis: Fork of https://code.google.com/p/ngs-analysis
ngs_pipeline: Exome/Capture/RNASeq Pipeline Implementation using snakemake
nihdatasciencesig.github.io: Creating data science community at NIH
Notes: Random notes/notebook
omicidx: null
PedsHemeOncBoardReview: null
pelicanHome: null
pelican-plugins: Collection of plugins for the Pelican static site generator
PIRetreat2014ComputePoster: An informal NCI PI Retreat about the Scientific Computing Interest Group
planets: These are my notes about planets.
precision_oncology_variant_resources_manuscript: Files for manuscript Resources for Interpreting Variants in Precision Genomic Oncology Applications
PresentationsFolder: null
project-open-source: null
PurdueBigTap2017: null
pybedtools: Python wrapper -- and more -- for Aaron Quinlan's BEDTools (bioinformatics tools)
pygments-code-block-directive: Definitions for a reStructuredText code-block directive using pygments, and scripts to render HTML and LaTeX.
PyVCF: A Variant Call Format reader for Python.
R4CancerDataSci: null
RCourseAWSStarter: null
rEutils: R package for accessing NCBI EUtilities
RForBioinformatics: null
Rgitbook: Gitbook for R Markdown
RNASeqBeginnerTutorial: null
RNASeqCompendium: Work in progress
rNCIGDC: null
r-pkgs: Building R packages
Rpressa: Miscellaneous R code for biological data tasks.
ruffus: A fork of the "ruffus" pipeline program
sbgr: R Client for Seven Bridges Genomics API
Scribl: HTML5 canvas genomic graphics library
scripts: Miscellaneous, uncategorized scripts
SDIntroToR: Introduction to R
SDST: null
seandavi.github.io: null
SeansStuff: Small example R package to teach R package development.
serpentine: null
shiny: null
shinydt: null
SimpleSnakemakeTutorial: null
SlurmPipelineWithDependencies: This is a simple slurm pipeline implemented in BASH that uses SLURM's dependency capabilities
SnakemakeKallisto: null
SnakemakeRNASeqExample: An example RNAseq pipeline with snakemake on the NIH biowulf cluster
snakemake-wrappers: null
snakewrappers: Snakemake wrappers, specifically designed for the NIH Biowulf system using TACC Modules
solr: A general purpose R interface to Solr
solvebio-python: SolveBio Python bindings
SQL_Tutorial_in_R: null
SRA2R: SRA2R, a package to import SRA data directly into R
SRAdb: Git mirror of Bioconductor SRAdb package
SRAdb-app: Server and UI files for SRAdp WebApp
SRAdbV2: R Interface to the NCBI SRA metadata
sshfs: File system based on the SSH File Transfer Protocol
support.bioconductor.org: Bioconductor's fork of the BiosStar Q&A site
swc-test: null
Talk_Graphs: Talk: How to display data badly
Talks: null
TARGETOsteoDataPackage: null
TARGOS: null
TeachingMaterial: Various teaching material
teamcgc.github.io: null
TenStepReproducible: Manuscript describing ten steps to reproducible analysis, work flows, and software in Bioconductor
terraform-emr-training: Terraform script for launching multiple EMR clusters for training purposes.
transfer-api-client-python: A Python client library for the Globus Online Transfer API
untar-to-s3: Script to unpack a tar file to an S3 bucket
vcf2maf: Convert VCF (Variant Call Format) into TCGA MAF (Mutation Annotation Format)
vcfanno: annotate a VCF with local or remote VCFs/BEDs/BAMs
VCFWrench: null
VCFWrenchR: Basic R package for VCF reformatting (json and tab-delimited text)
wdl-pcawg-bwa-mem-workflow: WDL implementation of https://github.com/ICGC-TCGA-PanCancer/Seqware-BWA-Workflow
wdlRunR: Elastic, reproducible, and reusable genomic data science tools from R backed by cloud resources

Commits To

Repository	Most Recent Commit	# Commits
seandavi/CompleteGenomicsTools	2017-05-22 14:50:27.0	1
seandavi/awesome-single-cell	2018-03-14 20:10:35.0	190
seandavi/awesome-cancer-variant-databases	2017-09-19 09:40:24.0	38
seandavi/wdlRunR	2017-10-04 18:13:51.0	98
Bioconductor/MultiOmicQC	2017-03-11 04:09:30.0	1
seandavi/ClinicalTrialsAPI	2017-03-21 01:44:01.0	4
seandavi/ci4cc-informatics-resources	2017-06-27 15:31:04.0	17

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.