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README.md
# TAPseq An R-package to design PCR primers for TAP-seq published in [Nature Methods, 2020](https://www.nature.com/articles/s41592-020-0837-5). `TAPseq` is available through [Bioconductor](http://bioconductor.org/packages/release/bioc/html/TAPseq.html). ## Installation This package requires local installations of Primer3 and BLASTn. `TAPseq` has been 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 and its R dependencies can be installed from Bioconductor using the `BiocManager` package. This requires `R >= 4.0.0`. ``` if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("TAPseq") ``` `TAPseq` can also be installed directly from GitHub using the `devtools` package. This also allows to install an older version, which work for `R >= 3.5`. ``` install.packages("devtools") # latest development version devtools::install_github("argschwind/TAPseq", dependencies = TRUE) # installing a previous version for R >= 3.5 devtools::install_github("argschwind/TAPseq@r_release_3.5", dependencies = TRUE) ``` ## 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") ```