ChIPseeker

https://github.com/yulab-smu/chipseeker

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This package implements functions to retrieve the nearest genes around the peak, annotate genomic...

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### Install ChIPseeker from Bioconductor

Source: https://github.com/yulab-smu/chipseeker/blob/devel/README.md

Install the released version of the ChIPseeker package using BiocManager. Ensure BiocManager is installed first if not already present.

```r
if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
## BiocManager::install("BiocUpgrade") ## you may need this
BiocManager::install("ChIPseeker")
```

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### Install ChIPseeker Development Version from GitHub

Source: https://github.com/yulab-smu/chipseeker/blob/devel/README.md

Install the development version of the ChIPseeker package directly from GitHub using the devtools package.

```r
## install.packages("devtools")
devtools::install_github("YuLab-SMU/ChIPseeker")
```

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### Distance to TSS for Positive Strand Genes

Source: https://github.com/yulab-smu/chipseeker/wiki/How-distanceToTSS-was-calculated

Calculates the minimum distance from a peak's start or end to a gene's start for genes on the positive strand. If the peak overlaps the gene, the distance is 0.

```R
## for genes in positive strand
min(start(peak) - start(gene), end(peak) - start(gene))
```

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### Distance to TSS for Negative Strand Genes

Source: https://github.com/yulab-smu/chipseeker/wiki/How-distanceToTSS-was-calculated

Calculates the minimum distance from a peak's start or end to a gene's end for genes on the negative strand. This accounts for the reversed coordinate system of negative strand genes.

```R
## for genes in negative strand
min(end(gene) - start(peak), end(gene) - end(peak))
```

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