inst/seqplots/www/help/Install_R.md

In seqplots: An interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and heatmaps

Installation - R/Bioconductor

The Bioconductor package runs SeqPlots locally on desktop computers from the R environment. It is available for Windows, GNU/Linux and Mac OS X operating systems. For further information please refer to SeqPlots Bioconductor webpage.

System requirements:

• R 3.1 or higher

How to install

To install SeqPlots package, start R and enter:

```{r eval=FALSE} if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("seqplots")

How to start
------------

To start SeqPlots web interface, start R and enter:

```{r eval=FALSE}
library(seqplots)
run()

After a successful initiation the user interface will be opened in your default web browser. For further usage please refer to Quick start guide or specific chapters.

The run function accepts "root" argument, which allows to change the data location folder (by default your home directory will be used), e.g.:

```{r eval=FALSE} run(root='/path/to/data/location')

### Additional genome packages

Genomic packages can be installed using standard bioconductor installer
(Internet connection is required). For example, to instal human reference
genome (hg19):

```{r eval=FALSE}
if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("BSgenome.Hsapiens.UCSC.hg19")

Genome packages are required before uploading files for plotting. Full list of supported genomes is avilable here: http://www.bioconductor.org/packages/release/BiocViews.html#___BSgenome

seqplots documentation built on Nov. 8, 2020, 4:52 p.m.