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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 Bioconductorsars2pack
An R package with over 50 highly cited, read-to-use, up-to-date COVID-19 pandemic data resourceswdlRunR
Elastic, reproducible, and reusable genomic data science tools from R backed by cloud resourcesSRAdbV2
R Interface to the NCBI SRA metadataci4cc-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 RSRAdb
Git mirror of Bioconductor SRAdb packageBiocPkgTools
Computable build reports, package metadata, and download stats from the Bioconductor projectngs-analysis
Fork of https://code.google.com/p/ngs-analysisngCGH
Tools for producing pseudo-cgh of next-generation sequencing dataOrchestra
workshop platform provider for running docker containers on kubernetesMachineLearningIntro
Machine learning use cases for teachingpostgresql_zombodb_docker
docker image containing postgresql and zombodb (pre-installed)BiocActions
Develop and host GitHub actions for BioconductorCompleteGenomicsTools
Software for manipulating and visualizing Complete Genomics data, with a focus on cancerngs
Next Gen Sequencing Utilitiesmethylumi
SDIntroToR
Introduction to RAtacSeqWorkshop
curatedMetagenomicsNextflow
Curated Metagenomics Data Nextflow workflowspubmed-llm-classifier
gpt-examplesserpentine
GEOmetadb
Github mirror of the GEOmetadb bioconductor packageconveyor
NGS pipelinesSimpleSnakemakeTutorial
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.emacs-d
My .emacs.d directoryCCR_NGS
Tools for next-generation sequencing in use at the CCR/NCInf-core-cmgd
ITR
Learning and teaching materials for R and BioconductorSDST
COSMIC.build57
An R data package for the COSMIC databaseGenomicSignatures
genetrack-central
GeneTrack is a genomic data visualization softwareawesome-variant-databases
A collection of genomic variant databasesClinicalTrialsAPI
Access the NIH ClinicalTrials.gov REST APITargetOsteoAnalysis
rEutils
R package for accessing NCBI EUtilitiessars2pack-book
Materials for sars2pack bookdown bookhour_of_code
Materials for Hour of Code using RInteractiveApps_Bioc2017
HarvardExtremeComputing
Materials for the Fall 2015 Harvard Extreme Computing courseOmicIDXR
Access the OmicIDX, a genomics metadata index project, from RRpressa
Miscellaneous R code for biological data tasks.bioDockerCollection
BiocGadgets
F1000R_BiocWorkflows
Project for publishing from Bioconductor to F1000R and backBiocIntegrativeCancerVis
SnakemakeRNASeqExample
An example RNAseq pipeline with snakemake on the NIH biowulf clusterOrchestratingSingleCellAnalysis
snakewrappers
Snakemake wrappers, specifically designed for the NIH Biowulf system using TACC Modulesterraform-can
terraform configuration files with focus on big data and genomicsRNASeqBeginnerTutorial
An introduction to RNA-seq file formats, quality control, and visualization targeted to a biologist audiencePedsHemeOncBoardReview
SlurmPipelineWithDependencies
This is a simple slurm pipeline implemented in BASH that uses SLURM's dependency capabilitiesteaching
BiocPkgToolsManuscript
MutationTools
MultiplatformGEOSurvey
A short use case for GEOmetadb and dplyrCuteCats
cmgd_web
Web portal and API for the Curated Metagenomics Data projectR4CancerDataSci
aisr-data-warehouse
Animal Image Shared Resource PACS/Viewerscripts
Miscellaneous, uncategorized scriptsold.seandavi.github.io
cmgd_coordinator
bigrna-pipeline
CollaborativeBookdown
An opinionated approach to building a collaborative bookdown bookbiodata18software
QFeaturesWorkshop2020
talks
genetics_branch_retreat_site
A small website generator for a conference that uses a google sheet to populate abstracts.Love Open Source and this site? Check out how you can help us