Niek Wit's Projects
BAGEL software
Application for making ENCODE Blacklists
CRISPR Analysis
Python script for backing up lab data to RCS
Pipeline for ChIP-Seq analsysis
Snakemake workflow for CRISPR-Cas9 screen analysis
Pipeline for CRISPR-Cas9 screen analysis
CRISPR-Cas screening docs
Pipeline for CUT&RUN analysis
Snakemake workflow for Cut & Run
Snakemake workflow for DamID-Seq analysis
An automated pipeline for processing DamID sequencing datasets
Downsample fastq files in an automated way
demultiplex utility for eclip raw fastq files (process eclip barcodes and ramdomers)
Python port of original find_peaks program in Perl. Find and merge significant peaks based on false discovery rate.
Tools for GC/MS
Quick mining and visualization of NGS data by integrating genomic databases
Files needed to process and analyse RNAseq data.
Designs oligos for custom sgRNA libraries
Pip package for CRISPR-Cas9 screen analysis
Tools for NGS data analysis
RNA-Seq pipeline
Snakemake workflow for RNA-Seq differential transcript analysis using Salmon/Deseq2