ChIPflow is a snakemake-based workflow for the analysis of ChIP-seq data from the raw fastq files to the differential analysis of transcription factor binding or histone modification marking. It streamlines critical steps like the quality assessment of the immunoprecipitation using the cross correlation and the replicate comparison for both narrow and broad peaks. For the differential analysis ChIPflow provides linear and non linear methods for normalisation between samples as well as conservative and stringent models for estimating the variance and testing the significance of the observed differences (see [chipuanar](https://gitlab.pasteur.fr/hub/chipuanar/)).
ChIPflow is a snakemake-based workflow for the analysis of ChIP-seq data from the raw fastq files to the differential analysis of transcription factor binding or histone modification marking. It streamlines critical steps like the quality assessment of the immunoprecipitation using the cross correlation and the replicate comparison for both narrow and broad peaks. For the differential analysis ChIPflow provides linear and non linear methods for normalisation between samples as well as conservative and stringent models for estimating the variance and testing the significance of the observed differences (see [chipflowr](https://gitlab.pasteur.fr/hub/chipflowr)).
## How to install ChIPflow ?
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@@ -48,7 +48,7 @@ In addition to above tools, you need to install pipeline-related tools:
- R >= 4.0.3
- spp == 1.15.2
- need following cran packages: snow, snowfail, bitops, caTools, RCurl, Rcpp, and bioconductor packages: GenomeInfoDB, genomicRanges, Rsamtools.
