Sebastian Gregoricchio

Codes associated to the analyses performed in Dauyey Velds et al., "A spatial single-cell transcriptomic atlas of metastatic breast cancer progression".

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

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.

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

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.

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

An R-package for power and sample size calculations for genomics data (ChIP-seq, ATAC-seq, CUT&Tag/RUN, etc.)

Sample drat repository for easy forking and bootstrapping

No description provided.

No description provided.

Enrichment Networks for Pathway Enrichment Analysis

Imputation of missing values of a matrix or data.frame using iterative prediction model

Snakemake pipline for the mapping and read count of RNA-seq data using STAR.

ChIP-seq pipeline specific for the Zwart lab

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

An R-package collection for nice colorPaletes

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

Conda recipes for the bioconda channel.

ChIP-seq Intersample Normalization

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