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:
Please install these tools first and add them to your
PATH. If you don't want to add the tools to
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
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)
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")
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