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.
STARna
Snakemake pipline for the mapping and gene read counting of RNA-seq data using STAR.
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.
power4peaks
An R-package for power and sample size calculcation for ChIP/ATAC/CUT&Tag data differential analyses.
Contact
For any information contact s.gregoricchio@nki.nl.
