Pinned Repositories
AnVILWorkflow
Runnable workflow package using Terra/GCP resources
AnVILWorkshop_initial
AnVIL/Terra workshop for BioC2020
awesome-drug-discovery-knowledge-graphs
A collection of research papers, datasets and software related to knowledge graphs for drug discovery. Accompanies the paper "A review of biomedical datasets relating to drug discovery: a knowledge graph perspective" (Briefings in Bioinformatics, 2022)
CNVWorkflow_Code
CNV analysis workflow code for the manuscript
CNVWorkflow_Meetup
2018 NYC R/Bioconductor Meetup Presentation
GenomicSuperSignature
Interpretation of RNAseq experiments through robust, efficient comparison to public databases
lefserBenchmarking
Benchmarking examples of lefser against LEfSe and microbiomeMarker
OmicsMLRepoR
Bioconductor package to access the harmonized metadata through ontology
PureCN_manuscript
HGNChelper
Identify and correct invalid gene symbols
shbrief's Repositories
shbrief/AnVILWorkshop_initial
AnVIL/Terra workshop for BioC2020
shbrief/ProjectAsPackage
Demonstration of the use of an R package to organize a data analysis project
shbrief/PureCN_Docker
Docker Image for PureCN R/Bioconductor Package
shbrief/1_mutect1_pon
Build a pool of normal (PoN) using MuTect v.1.1.7
shbrief/1_mutect1_variants_calling
SNV/SNP calling using MuTect v.1.1.7
shbrief/1_purecn_intervalfile
Build interval file for PureCN run from BED and mappability files
shbrief/2019_scWorkshop
Repo for Physalia course Analysis of Single Cell RNA-Seq data
shbrief/3_purecn_normaldb
Build normalDB for CNV workflow using PureCN
shbrief/4_purecn_purecn
shbrief/5_purecn_dx
PureCN Dx.R for extracting copy number and mutation metrics
shbrief/academic-kickstart
shbrief/BioBombe
BioBombe: Sequentially compressed gene expression features enhances biological signatures
shbrief/bioc_docker
Docker containers for Bioconductor
shbrief/BiocPkgTools
Computable build reports, package metadata, and download stats from the Bioconductor project
shbrief/cheatsheet-gcp-A4
:cloud: GCP gcloud, gsutil, etc.
shbrief/CNVworkflow_Terra_WDL
CNV analysis workflows for Terra workspace
shbrief/curatedcrcdata
shbrief/dropEst
Pipeline for initial analysis of droplet-based single-cell RNA-seq data
shbrief/dynmethods
A collection of 50+ trajectory inference methods within a common interface 📥📤
shbrief/grip
Graph Integration Platform
shbrief/Hackathon
Multi-omics studies are available here
shbrief/leonardo
Notebook service
shbrief/minimal-mistakes
:triangular_ruler: Jekyll theme for building a personal site, blog, project documentation, or portfolio.
shbrief/MOFA
Multi-Omics Factor Analysis
shbrief/MOFA2
Multi-Omics Factor Analysis V2 (MOFA+)
shbrief/MungeCuratedMGS
shbrief/pavian
🌈 Interactive analysis of metagenomics data
shbrief/r
Using R with Jupyter / RStudio on Binder
shbrief/sysreqs
R package to install system requirements
shbrief/velocyto.R
RNA velocity estimation in R