Brian Lohman's repositories
brianlohman.github.io
Personal Website
cellranger-nf
A Nextflow wrapper for 10X Cellranger to wrangle the 10,000+ output files per sample
clinical-components
Summarize the clinical (or lab) components and correlations of your dataset.
ctseq-nf
A Nextflow wrapper for ctseq
Docker
Docker containers for various purposes
nim_tools
Collection of in progress tools for genomics with nim
py_tools
Collection of in progress scripts for genomics with python
RNAseq-variant-calling-nf
A Nextflow workflow to call variants with GATK from bulk RNAseq data
SingleCellGarage
My R package of utilities for working with single cell data
star-rsem-scrnaseq-nf
Run STAR and RSEM on scRNAseq data demultiplexed by cell barcode
pdx-nf
A Nextflow workflow to generate gene counts from PDX bulk RNAseq data
R_tools
A collection of scripts in progress
sarek
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
workflows
Workflows with Nextflow