INSTALL.md

In TSRchitect: Promoter identification from large-scale TSS profiling data

TSRchitect Installation and Setup

Preliminary Steps

TSRchitect is a package for the R software environment for statistical computing. We assume that you have a current version of R installed and are familiar with its use. Several other packages are prerequisite for TSRchitect, and these packages are available through CRAN or Bioconductor. Typical preliminary steps to install or update these packages are as follows (note: for system-wide installation, you would need to invoke R as root):

```{r eval=FALSE}

installing CRAN packages

install.packages(c("gtools","knitr"))

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

installing Bioconductor packages

BiocManager::install(c("AnnotationHub", "BiocGenerics", "BiocParallel", "ENCODExplorer", "GenomicAlignments", "GenomeInfoDb", "GenomicRanges", "IRanges", "Rsamtools", "rtracklayer", "S4Vectors", "SummarizedExperiment"))

## Obtaining TSRchitect
__TSRchitect__ is available as a
[Bioconductor](http://bioconductor.org/) package and thus can be installed in
the same way as the prerequisite packages:

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

Optionally, you can install TSRchitect directly from our group's GitHub repository as follows (again, use root privileges on the install command for system-wide installation):

```{bash eval=FALSE} git clone https://github.com/BrendelGroup/TSRchitect R CMD INSTALL TSRchitect

Note that the `master` branch should be a stable version, possibly somewhat
ahead of the Biocondcutor version in case of minor edits or addtions.
You may also see a `devel` branch, which would contain recently developed
addtions that are not yet fully tested.
To clone and install just the 'devel' branch, please do the following:
```{bash eval=FALSE}
git clone https://github.com/BrendelGroup/TSRchitect --branch devel --single-branch
R CMD INSTALL TSRchitect

In either case, please use the GitHub Issues button to report problems or suggest novel features.

Installation as a singularity container

Assuming a current version of singularity is installed on your system (if not, it should be, and it's easy to do so), you can get the TSRchitect container from Singularity Hub as follows:

singularity pull --name tsr.simg shub://BrendelGroup/TSRchitect

For a gentle introduction to singularity, see our group handbook article.

Finally

Proceed to the TSRchitectUsersGuide for examples of how the use TSRchitect functions. If you are interested in developing and running entire workflows for transcription start site profiling, please see our paper or simple worked examples in the HOWTO document.

TSRchitect documentation built on Nov. 8, 2020, 8:11 p.m.