• Stars
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    22
  • Rank 1,043,841 (Top 21 %)
  • Language
  • License
    MIT License
  • Created over 7 years ago
  • Updated over 2 years ago

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Repository Details

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

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Bioc2017BigDataWorkshopSession

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SRAdb

Git mirror of Bioconductor SRAdb package
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BiocPkgTools

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

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ngCGH

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Orchestra

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MachineLearningIntro

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BiocActions

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CompleteGenomicsTools

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

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SDIntroToR

Introduction to R
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AtacSeqWorkshop

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curatedMetagenomicsNextflow

Curated Metagenomics Data Nextflow workflows
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pubmed-llm-classifier

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serpentine

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GEOmetadb

Github mirror of the GEOmetadb bioconductor package
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conveyor

NGS pipelines
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SimpleSnakemakeTutorial

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VCFWrenchR

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

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nextflow_on_jupyter

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

My .emacs.d directory
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CCR_NGS

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

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33

ITR

Learning and teaching materials for R and Bioconductor
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SDST

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COSMIC.build57

An R data package for the COSMIC database
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GenomicSignatures

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genetrack-central

GeneTrack is a genomic data visualization software
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awesome-variant-databases

A collection of genomic variant databases
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ClinicalTrialsAPI

Access the NIH ClinicalTrials.gov REST API
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TargetOsteoAnalysis

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rEutils

R package for accessing NCBI EUtilities
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sars2pack-book

Materials for sars2pack bookdown book
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43

hour_of_code

Materials for Hour of Code using R
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InteractiveApps_Bioc2017

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HarvardExtremeComputing

Materials for the Fall 2015 Harvard Extreme Computing course
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OmicIDXR

Access the OmicIDX, a genomics metadata index project, from R
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47

Rpressa

Miscellaneous R code for biological data tasks.
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48

bioDockerCollection

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49

BiocGadgets

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F1000R_BiocWorkflows

Project for publishing from Bioconductor to F1000R and back
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BiocIntegrativeCancerVis

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52

SnakemakeRNASeqExample

An example RNAseq pipeline with snakemake on the NIH biowulf cluster
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OrchestratingSingleCellAnalysis

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snakewrappers

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

terraform configuration files with focus on big data and genomics
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terraform_vertex_ai_project

Terraform for allowing gcp Vertex AI for a user
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PedsHemeOncBoardReview

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SlurmPipelineWithDependencies

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

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BiocPkgToolsManuscript

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MutationTools

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MultiplatformGEOSurvey

A short use case for GEOmetadb and dplyr
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CuteCats

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cmgd_web

Web portal and API for the Curated Metagenomics Data project
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R4CancerDataSci

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aisr-data-warehouse

Animal Image Shared Resource PACS/Viewer
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scripts

Miscellaneous, uncategorized scripts
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RNASeqBeginnerTutorial

An introduction to RNA-seq file formats, quality control, and visualization targeted to a biologist audience
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old.seandavi.github.io

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cmgd_coordinator

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bigrna-pipeline

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CollaborativeBookdown

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biodata18software

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QFeaturesWorkshop2020

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genetics_branch_retreat_site

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