Commit 3e7e727d authored by Rachel  LEGENDRE's avatar Rachel LEGENDRE
Browse files

add workflow image - correct some typo in chipflowR

parent 9b82c3f2
......@@ -14,7 +14,7 @@
ePeak is a snakemake-based workflow for the analysis of ChIP-seq data from raw FASTQ files to 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 ePeak 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)).
<img src="images/ePeak_pipeline.svg" width="700">
<img src="images/epeak_workflow.png" width="700">
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---
#logopath: "inst/Logos_LogoC3BI.png" #system.file("Logos_LogoC3BI.png", package = "ChIPflow")
title: "ChIPflow differential analysis report"
title: "ePeak differential analysis report"
date: '`r Sys.Date()`'
output:
html_document:
......@@ -18,7 +18,7 @@ bibliography: bibliography.bib
csl: medecine-sciences.csl
---
This report is generated by ChIPflowR, and R package included in ChIPflow a Snakemake pipeline for ChIP-seq data. ChIPflowR is an adaptation of the SARTools R package [@Varet2016] and is freely available at https://gitlab.pasteur.fr/hub/chipflowr. If you use ChIPflow and/or ChIPflowR please cite: M. Daunesse, R Legendre, H. Varet, A. Pain, C. Chica. 2021. _ChIPflow: from raw data to epigenomic dynamics_, bioRxiv.
This report is generated by ChIPflowR, and R package included in ePeak a Snakemake pipeline for ChIP-seq data. ChIPflowR is an adaptation of the SARTools R package [@Varet2016] and is freely available at https://gitlab.pasteur.fr/hub/chipflowr. If you use ePeak and/or ChIPflowR please cite: M. Daunesse, R Legendre, H. Varet, A. Pain, C. Chica. 2021. _ChIPflow: from raw data to epigenomic dynamics_, bioRxiv.
```{r echo=FALSE, results="asis", results="hide", message=FALSE, warning=FALSE}
# Package
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