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.
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")
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")