owenwilkins

pyflow-ChIPseq

a snakemake pipeline to process ChIP-seq files from GEO or in-house

bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

jp_gene_viz

A collection of visualizations for genomics related information for use with Jupyter notebooks.

ILCnetworks

Gene regulatory networks for intestinal innate lymphoid cells

infTRN_lassoStARS

Transcriptional regulatory network inference from gene expression and prior information with LASSO-StARS

scRNAseq_Benchmark

Bench-marking classification tools for scRNA-seq data

atac-seq-pipeline

ENCODE ATAC-seq pipeline

gtex-pipeline

GTEx & TOPMed data production and analysis pipelines

grape-nf

An automated RNA-seq pipeline using Nextflow

Awesome-Bioinformatics

A curated list of awesome Bioinformatics libraries and software.

rnaseq-star-rsem-pipeline

STAR-RSEM pipeline for RNA-seq data processing

toil-rnaseq

UC Santa Cruz Computational Genomics Lab's Toil-based RNA-seq pipeline

RefFreeEWAS

RefFreeEWAS (R package on CRAN)

pipeline

bradner lab computation pipeline scripts

shinyCircos

an R/shiny application for creation of Circos plot interactively

pyfaidx

Efficient pythonic random access to fasta subsequences

fastqp

Simple FASTQ quality assessment using Python

biopython

Official git repository for Biopython (originally converted from CVS)

adam

ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.

galaxy

Data intensive science for everyone.

HNSCC-miRSNP-Survival

Normal-breast-5hmC

OxyBS

Vignette for data processing and use of the fitOxBS function from the OxyBS R package

shared_450K_annotation

Lab-Tutorials

Programming tutorials for the Christensen Lab