# TAPseq
An R-package to design PCR primers for TAP-seq. The **master** branch is used for a submission to
Bioconductor. Please use the **r_release_3.5** branch to install the package for current R releases.
## Installation
This package requires local installations of Primer3 and BLASTn. TAPseq was developed and tested
using Primer3 v.2.5.0 and blastn v.2.6.0. It's strongly suggested to use Primer3 >= 2.5.0! Earlier
versions require a primer3_config directory, which needs to be provided whenever calling functions
interacting with Primer3. Source code and installation instructions can be found under:
Primer3: <https://github.com/primer3-org/primer3/releases>
BLASTn: <https://www.ncbi.nlm.nih.gov/books/NBK279690/>
Please install these tools first and add them to your `PATH`. If you don't want to add the tools to
your "global" `PATH`, you can add the following code to an `~/.Rprofile file`. This should add the
tools to your `PATH` in R whenever you start a new session.
```
Sys.setenv(PATH = paste("/full/path/to/primer3-x.x.x/src", Sys.getenv("PATH"), sep = ":"))
Sys.setenv(PATH = paste("/full/path/to/blast+/ncbi-blast-x.x.x+/bin", Sys.getenv("PATH"),
sep = ":"))
```
The R-package itself and its R dependencies can be installed from the Bioconductor devel branch
using the `BiocManager` package. This requires R >= 4.0.0.
```
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("TAPseq", version = "devel")
```
## Examples
An example of the TAPseq primer design workflow can be found in a vignette. To view the vignette,
run the following command (assuming vignettes were built when the package was installed).
```
vignette("tapseq_primer_design", package = "TAPseq")
```
Examples of how to select and evaluate target genes to identify cell populations can be found in
a separate vignette. This requires that the additional dependencies are installedl, which should be
the case if the package was installed with building vignettes and suggested dependencies.
```
vignette("tapseq_target_genes", package = "TAPseq")
```
