monovich

cutandrun

Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream analysis.

ICRG

Example code to generate the In-silico Combined human-mouse Reference Genome (ICRG) to distinguish human and mouse reads in high-throughput sequencing experiments

micromamba-docker

Rapid builds of small Conda-based containers using micromamba.

mageck

Experimental source code for MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout)

fetch

Download files, folders, and release assets from a specific git commit, branch, or tag of public and private GitHub repos.

r-optparse

command-line optional argument parser

littler

A scripting and command-line front-end for GNU R

CB2

CB2 is an R package which provides functions for hit gene identification and quantification of sgRNA (single-guided RNA) abundances for CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) pooled screen data analysis. Details are in Jeong et al. (2019) <doi:10.1101/gr.245571.118> and Baggerly et al. (2003) <doi:10.1093/bioinformatics/btg173>.

singularity-homer

HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.

rna-seq-star-deseq2

RNA-seq workflow using STAR and DESeq2

bedtools2

bedtools - the swiss army knife for genome arithmetic

ChIP-Seq-pipeline-Flux-

SnakeMake pipeline for ChIP-Seq alignment, filtering, display files, peak calling and motif analysis

CRISPRi_pipeline

Snakemake pipeline for processing CRISPRi screens

ghrKO_lysosome_targetomics

ghrKO_lysosome_targetomics

giblin-sirt5-melanoma

Supporting Code, Files, & Documentation For Giblin et al., 2020

bart2-docker

Run BARTv2.0 in a Docker Container

ChIPseq_ATACseq_pipelines

Snakemake pipelines for ChIPseq and ATACseq experiments

intro-to-snakemake

marge

API for HOMER in R for Genomic Analysis using Tidy Conventions

Terraria-Map-Editor

TEdit - Terraria Map Editor - TEdit is a stand alone, open source map editor for Terraria. It lets you edit maps just like (almost) paint! It also lets you change world settings (time, bosses downed etc), edit chests and change sign, make epic dungeons, castles, cities, and add rewards for your adventurers!

MSqRobHurdlePaper

normalize_bedgraph

Normalize bedgraph files

MendelianRNA-seq

kentUtils

UCSC command line bioinformatic utilities

islet_sci-ATAC-seq_2019

Code accompanying Islet sci-ATAC-seq project

ataqv

A toolkit for QC and visualization of ATAC-seq results.

Snakemake_ATAC-seq

ATAC-seq processing pipeline in Snakemake form

bwa

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

bwa-mem2

The next version of bwa-mem