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Sean Davis (@seandavi)

seandavi

Stars
3,409
Global Rank 8,498 (Top 0.3 %)
Followers 754
Following 40
Registered over 15 years ago
Most used languages

R
34.4 %

Python
23.4 %

HTML
10.9 %

Dockerfile
6.3 %

Shell
6.3 %

TeX
4.7 %

Nextflow 4.7 %

HCL 3.1 %

Jupyter Notebook
1.6 %

Emacs Lisp
1.6 %

CSS
1.6 %

JavaScript
1.6 %
Location 🇺🇸 United States
Country Total Rank 3,051
Country Ranking

Nextflow 15

R
190

Dockerfile
515

Emacs Lisp
948

HCL 1,367

TeX
1,716

HTML
7,026

Python
8,383

Shell
8,504

awesome-single-cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

awesome-cancer-variant-databases

A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.

GEOquery

The bridge between the NCBI Gene Expression Omnibus and Bioconductor

sars2pack

An R package with over 50 highly cited, read-to-use, up-to-date COVID-19 pandemic data resources

wdlRunR

Elastic, reproducible, and reusable genomic data science tools from R backed by cloud resources

SRAdbV2

R Interface to the NCBI SRA metadata

ci4cc-informatics-resources

Community-maintained list of resources that the CI4CC organization and the larger cancer informatics community have found useful or are developing.

Bioc2017BigDataWorkshopSession

Tutorial for working with cloud infrastructure and AWS from R

SRAdb

Git mirror of Bioconductor SRAdb package

BiocPkgTools

Computable build reports, package metadata, and download stats from the Bioconductor project

ngs-analysis

Fork of https://code.google.com/p/ngs-analysis

ngCGH

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

Orchestra

workshop platform provider for running docker containers on kubernetes

MachineLearningIntro

Machine learning use cases for teaching

postgresql_zombodb_docker

docker image containing postgresql and zombodb (pre-installed)

BiocActions

Develop and host GitHub actions for Bioconductor

CompleteGenomicsTools

Software for manipulating and visualizing Complete Genomics data, with a focus on cancer

ngs

Next Gen Sequencing Utilities

methylumi

SDIntroToR

Introduction to R

AtacSeqWorkshop

curatedMetagenomicsNextflow

Curated Metagenomics Data Nextflow workflows

pubmed-llm-classifier

serpentine

GEOmetadb

Github mirror of the GEOmetadb bioconductor package

conveyor

SimpleSnakemakeTutorial

VCFWrenchR

Basic R package for VCF reformatting (json and tab-delimited text)

textvision

nextflow_on_jupyter

A lightweight introduction to NextFlow, a workflow description language and engine for (mainly) bioinformatics workflows. Leverages notebooks for easy teaching.

Jupyter Notebook

emacs-d

My .emacs.d directory

CCR_NGS

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

nf-core-cmgd

ITR

Learning and teaching materials for R and Bioconductor

SDST

COSMIC.build57

An R data package for the COSMIC database

GenomicSignatures

genetrack-central

GeneTrack is a genomic data visualization software

awesome-variant-databases

A collection of genomic variant databases

ClinicalTrialsAPI

Access the NIH ClinicalTrials.gov REST API

TargetOsteoAnalysis

rEutils

R package for accessing NCBI EUtilities

sars2pack-book

Materials for sars2pack bookdown book

hour_of_code

Materials for Hour of Code using R

InteractiveApps_Bioc2017

HarvardExtremeComputing

Materials for the Fall 2015 Harvard Extreme Computing course

OmicIDXR

Access the OmicIDX, a genomics metadata index project, from R

Rpressa

Miscellaneous R code for biological data tasks.

bioDockerCollection

BiocGadgets

F1000R_BiocWorkflows

Project for publishing from Bioconductor to F1000R and back

BiocIntegrativeCancerVis

SnakemakeRNASeqExample

An example RNAseq pipeline with snakemake on the NIH biowulf cluster

OrchestratingSingleCellAnalysis

snakewrappers

Snakemake wrappers, specifically designed for the NIH Biowulf system using TACC Modules

terraform-can

terraform configuration files with focus on big data and genomics

terraform_vertex_ai_project

Terraform for allowing gcp Vertex AI for a user

RNASeqBeginnerTutorial

An introduction to RNA-seq file formats, quality control, and visualization targeted to a biologist audience

PedsHemeOncBoardReview

SlurmPipelineWithDependencies

This is a simple slurm pipeline implemented in BASH that uses SLURM's dependency capabilities

teaching

BiocPkgToolsManuscript

MutationTools

MultiplatformGEOSurvey

A short use case for GEOmetadb and dplyr

CuteCats

cmgd_web

Web portal and API for the Curated Metagenomics Data project

R4CancerDataSci

aisr-data-warehouse

Animal Image Shared Resource PACS/Viewer

scripts

Miscellaneous, uncategorized scripts

old.seandavi.github.io

cmgd_coordinator

bigrna-pipeline

CollaborativeBookdown

An opinionated approach to building a collaborative bookdown book

biodata18software

QFeaturesWorkshop2020

talks

genetics_branch_retreat_site

A small website generator for a conference that uses a google sheet to populate abstracts.