niekwit

pycrispr

Pip package for CRISPR-Cas9 screen analysis

rna-seq-salmon-deseq2

Snakemake workflow for RNA-Seq differential transcript analysis using Salmon/Deseq2

snakefetch

A tool to fetch workflow and config files from a Snakemake repository on GitHub

camrcs

Python script for backing up lab data to RCS

crispr-screens

Snakemake workflow for CRISPR-Cas9 screen analysis

crispr_docs

CRISPR-Cas screening docs

cut_and_run

Snakemake workflow for Cut & Run

damid-seq

Snakemake workflow for DamID-Seq analysis

os_setup

pycod

Designs oligos for custom sgRNA libraries

pyseqtools

Tools for NGS data analysis

rna-seq-star-tetranscripts

Snakemake workflow for transposable element RNA-Seq using TEtranscripts

seq-tools

eclipdemux

demultiplex utility for eclip raw fastq files (process eclip barcodes and ramdomers)

find_peaks_py

Python port of original find_peaks program in Perl. Find and merge significant peaks based on false discovery rate.

GC-MS-tools

Tools for GC/MS

ms_tools

niekwit.github.io

RNA-Seq

RNA-Seq pipeline

snakemake-wrappers

USP43

bioinformatic-one-liners

Blacklist

Application for making ENCODE Blacklists

ChIP-Seq-pipeline

Pipeline for ChIP-Seq analsysis

CRISPR-tools

Pipeline for CRISPR-Cas9 screen analysis

CUT-RUN

Pipeline for CUT&RUN analysis

damidseq_pipeline

An automated pipeline for processing DamID sequencing datasets

KRAS-RIT1-profiling

scripts_ravi

snakesuite

Multiple NGS snakemake workflows