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Repositories

CUTEmake

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

multiDUMP

A simple snakemake based pipeline to parallelize the download of SRA data through 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.

SPACCa

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

snakeATAC

Snakemake pipeline for analysis and normalization of ATAC-seq data starting from fastq.gz files. It includes the possibility to call SNPs and InDels at ATAC-seq peaks (tested only for human samples).

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.

Contact

For any information contact s.gregoricchio@nki.nl.

https://orcid.org/0000-0001-9209-5403

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