GitHub - argschwind/TAPseq: R package to design PCR primers for TAP-seq (original) (raw)

TAPseq

An R-package to design PCR primers for TAP-seq published inNature Methods, 2020. TAPseq is available through Bioconductor.

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 BiocManagerpackage. 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")