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Pipelines

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.

SPACCa

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

Zwart lab modified version: ChIP_Zwart. (works only on NKI servers because annotations paths are hard-coded)

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.

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R-packages

DEprot

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

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.

Contact

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

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

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