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# 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: <> BLASTn: <> 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") ```