sebastian-gregoricchio

snHiC

Snakemake pipeline for analysis and normalization of Hi-C data starting from fastq.gz files. It includes the possibility to perform grouped analyses, TAD, loops and stripes detections, as well as differential compartment and chromatin interaction analyses.

snakeATAC

Snakemake pipeline for analysis and normalization of ATAC-seq data starting from fastq.gz files.

bioconda-recipes

Conda recipes for the bioconda channel.

ChIP_Zwart

ChIP-seq pipeline specific for the Zwart lab

CHIPIN

ChIP-seq Intersample Normalization

CUTEmake

Snakemake pipeline for analysis and normalization (without SPIKE-IN) of CUT&Tag data starting from fastq.gz files.

DEprot

Package to impute, normalize and perform differential analyses on proteomics data (LFQ-based)

multiDUMP

Easy to use snakmake function to run the parallel download of SRA runs via fastq-dump.

Rseb

An R-package for daily tasks required to handle biological data as well as avoid re-coding of small functions for quick but necessary data management.

sebastian-gregoricchio.github.io

selfish

SELFISH is a tool for finding differential chromatin interactions between two Hi-C contact maps.

SPACCa

Snakemake Pipeline for the Analyses of ChIP-seq data in Cancer samples