bkohrn

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

Duplex-Sequencing

generalDockerEnvs

A place for various containers I've put together for use in various pipelines.

LoebLab

Stuff from DuplexSequencing for LoebLab

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.

pysam

Pysam is a Python module for reading and manipulating SAM/BAM/VCF/BCF files. It's a lightweight wrapper of the htslib C-API, the same one that powers samtools, bcftools, and tabix.

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