README.md

In kathrynrozengagnon/CLIPflexR: CLIP tools and wrappers in R

Readme

CLIPflexR is a R wrapper for the CLIP Tool Kit (CTK) and additional functions to call other external libraries into an R environment.

CLIPflexR makes use of the Herper library to install conda dependencies to your machine within a conda environment using the reticulate libraries.

The CTK toolkit is installed as part of the CLIPflexR install_ctk() function.

How to install CLIPflexR

install.packages("devtools")
devtools::install_github("kathrynrozengagnon/CLIPflexR")
devtools::install_github("RockefellerUniversity/Herper")
Herper::install_CondaSysReqs("CLIPflexR")
CLIPflexR::install_ctk()

Path to Conda tools and CTK/czplib

library(CLIPflexR)

## CLIPflexR_0.1.18 conda env found at /Users/kathryn/Library/r-miniconda/envs/CLIPflexR_0.1.18

## ctk found  at /Users/kathryn/Library/r-miniconda/envs/CLIPflexR_0.1.18/bin/ctk

## czplib found  at /Users/kathryn/Library/r-miniconda/envs/CLIPflexR_0.1.18/lib/czplib

getOption("CLIPflexR.condaEnv")

## [1] "/Users/kathryn/Library/r-miniconda/envs/CLIPflexR_0.1.18"

getOption("CLIPflexR.ctk")

## [1] "/Users/kathryn/Library/r-miniconda/envs/CLIPflexR_0.1.18/bin/ctk"

getOption("CLIPflexR.czplib")

## [1] "/Users/kathryn/Library/r-miniconda/envs/CLIPflexR_0.1.18/lib/czplib"

See our vignettes for installing CLIPflexR, or processing CLIP data using CTK or CLIPflexR. You can also mix and match!

Please bear with us while we update examples and vignettes, more coming soon....

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kathrynrozengagnon/CLIPflexR documentation built on Dec. 8, 2022, 7:31 p.m.