Sean Davis

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

awesome-cancer-variant-resources. 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

GFFutils. Convert, explore, and manipulate GFF and GTF files (used in bioinformatics) using a sqlite-based approach

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

ols-mcp-server. A model context protocol (MCP) server for the EBI Ontology Lookup Service (OLS)

SRAdb. Git mirror of Bioconductor SRAdb package

SRAdbV2. R Interface to the NCBI SRA metadata

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

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

Orchestra. workshop platform provider for running docker containers on kubernetes

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

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

MachineLearningIntro. Machine learning use cases for teaching

BiocActions. Develop and host GitHub actions for Bioconductor

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

postgresql_zombodb_docker. docker image containing postgresql and zombodb (pre-installed)

RBiocBook. An instructional/experiential book using R and Bioconductor.

curatedMetagenomicsNextflow. Curated Metagenomics Data Nextflow workflows

ngs. Next Gen Sequencing Utilities

methylumi. R

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

AtacSeqWorkshop. R

pubmed-llm-classifier. gpt-examples

SDIntroToR. Introduction to R

amc-ai-governance. Book -- Implementing AI at an Academic Medical Center

GEOmetadb. Github mirror of the GEOmetadb bioconductor package

conveyor. NGS pipelines

SimpleSnakemakeTutorial. Shell

serpentine. Python

emacs-d. My .emacs.d directory

textvision. Python

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

ClinicalTrialsAPI. Access the NIH ClinicalTrials.gov REST API

ITR. Learning and teaching materials for R and Bioconductor

TargetOsteoAnalysis. HTML

GenomicSignatures. R

genetrack-central. GeneTrack is a genomic data visualization software

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

InteractiveApps_Bioc2017. R

refinebioc. The bridge between refine.bio and Bioconductor

terraform_vertex_ai_project. Terraform for allowing gcp Vertex AI for a user