bkohrn's repositories
bioconda-recipes
Conda recipes for the bioconda channel.
cellprofiler-nf
A nextflow pipeline to run CellProfiler pipelines on raw images and process output
Duplex-Seq-Pipeline
A standalone end-to-end data analysis pipeline for Duplex Sequencing
generalDockerEnvs
A place for various containers I've put together for use in various pipelines.
maftools
Summarize, Analyze and Visualize MAF files from TCGA or in house studies.
multi-fastqc-nf
Workflow running FastQC across multiple files
picard_demux_nextflow
A nextflow pipeline for demultiplexing using picardtools.
picard_demux_snakemake
A quick Snakemake pipeline for converting BCL files to fastq and unaligned bam files.
samwell
Samwell: a python package for using genomic files... well
VarDictJava
VarDict Java port
vcf2maf
Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
workflow-template-nextflow
Template for building a small workflow in Nextflow