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bagel

BAGEL software

bioinformatic-one-liners

blacklist

Application for making ENCODE Blacklists

cam

CRISPR Analysis

camrcs

Python script for backing up lab data to RCS

chip-seq-pipeline

Pipeline for ChIP-Seq analsysis

crispr-oligo-designer

crispr-screens

Snakemake workflow for CRISPR-Cas9 screen analysis

crispr-tools

Pipeline for CRISPR-Cas9 screen analysis

crispr_docs

CRISPR-Cas screening docs

cut-run

Pipeline for CUT&RUN analysis

cut_and_run

Snakemake workflow for Cut & Run

damid-seq

Snakemake workflow for DamID-Seq analysis

damidseq_pipeline

An automated pipeline for processing DamID sequencing datasets

dogfinder

downsampling

Downsample fastq files in an automated way

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

kras-rit1-profiling

ms_tools

ngsplot

Quick mining and visualization of NGS data by integrating genomic databases

niekwit.github.io

os_setup

pragui-fork

Files needed to process and analyse RNAseq data.

pycod

Designs oligos for custom sgRNA libraries

pycrispr

Pip package for CRISPR-Cas9 screen analysis

pyseqtools

Tools for NGS data analysis

rna-seq

RNA-Seq pipeline

rna-seq-salmon-deseq2

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