All code in this package has been tested on R 3.6.0 and 4.4.1, but any version of R 3.x or 4.x should be compatible. Other package versions may have impact the use of httrpathway due to changes in functionality, function parameter updates (e.g. GSVA), or changes in API.
httrpathway is currently implemented as an in-development R package and can be installed using the devtools R package (http://devtools.r-lib.org/):
Local installation:
- Clone or download the package from github (TBD):
git clone https://github.com/USEPA/CompTox-httrpathway.git- Install the package using devtools functions in R/Rstudio:
#load devtools library
library(devtools)
#use devtools functions to load package and documentation
devtools::install_local(path = "/path/to/httrpathway/", force = TRUE)
library(httrpathway)Using devtools::install_github():
- Run devtools function to install directly from Github
#load devtools library
library(devtools)
#install from Github
devtools::install_github("USEPA/CompTox-httrpathway")Please see the httrpathway vignette (/httrpathway/vignettes/httrpathway-vignette.Rmd) for instructions for how to execute the core functions of httrpathway. This includes an overview of the structure of the log2 fold-change tables httrpathway expects as input, as well as how to run the core concentration-response analysis of high-throughput transcriptomics (HTTr) data for either signature/pathways or genes/probes.
v0.2.1 (4/8/2025)
- Fixed bug in how geneConcResp function estimates the baseline to use
conc_index <= 2instead ofconc <= 0.1
v0.2 (2/6/2025)
- Various code improvements
- Improved roxygen2 documentation
- devtools package load functions work as intended
- Refined documentation including manual and vignette
- Deprecated many non-core functions
v0.1 (12/13/2021)
- Initial commit from public Github repo (12/13/2021)
- Derik E. Haggard
- Joseph Bundy
- Logan J. Everett
- Lionel Girardin
- Richard Judson