Pinned 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
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.
CallHap
A bioinformatics pipeline for processing of population-level pooled chloroplast DNA
Duplex-Sequencing
pysam
Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.
bkohrn's Repositories
bkohrn/bioconda-recipes
Conda recipes for the bioconda channel.
bkohrn/cellprofiler-nf
A nextflow pipeline to run CellProfiler pipelines on raw images and process output
bkohrn/Duplex-Seq-Pipeline
A standalone end-to-end data analysis pipeline for Duplex Sequencing
bkohrn/Duplex-Sequencing
bkohrn/generalDockerEnvs
A place for various containers I've put together for use in various pipelines.
bkohrn/LoebLab
Stuff from DuplexSequencing for LoebLab
bkohrn/maftools
Summarize, Analyze and Visualize MAF files from TCGA or in house studies.
bkohrn/multi-fastqc-nf
Workflow running FastQC across multiple files
bkohrn/picard_demux_nextflow
A nextflow pipeline for demultiplexing using picardtools.
bkohrn/picard_demux_snakemake
A quick Snakemake pipeline for converting BCL files to fastq and unaligned bam files.
bkohrn/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.
bkohrn/samwell
Samwell: a python package for using genomic files... well
bkohrn/VarDictJava
VarDict Java port
bkohrn/vcf2maf
Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
bkohrn/workflow-template-nextflow
Template for building a small workflow in Nextflow