diff --git a/DESCRIPTION b/DESCRIPTION index 936a245..58f6b11 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: dominoSignal Title: Cell Communication Analysis for Single Cell RNA Sequencing -Version: 0.99.3 +Version: 0.99.4 Authors@R: c( person("Christopher", "Cherry", role = c("aut"), email = "ccherry.6574@gmail.com", comment = c(ORCID = "0000-0002-5481-0055")), person("Jacob T", "Mitchell", role = c("aut", "cre"), email = "jmitch81@jhmi.edu", comment = c(ORCID = "0000-0002-5370-9692")), diff --git a/NEWS.md b/NEWS.md index e8fa263..41de1fd 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,9 @@ +# dominoSignal v0.99.4 + +## Vignettes + +- Updated download instructions to use the bioconductor URL + # dominoSignal v0.99.3 ## create_domino Function Warnings diff --git a/tests/testthat/test-regression.R b/tests/testthat/test-regression.R index 87911d8..552ee3d 100644 --- a/tests/testthat/test-regression.R +++ b/tests/testthat/test-regression.R @@ -3,7 +3,7 @@ ## large scale test that processing functions generate results matching the state of the code in v0.2.1 test_that("creation of rl_map from CellPhoneDB v4 input", { - # use rl_map created in domino2 v0.2.1 + # use rl_map created in dominoSignal v0.2.1 rl_map <- create_rl_map_cellphonedb( genes = v0.2.1$genes_tiny, proteins = v0.2.1$proteins_tiny, @@ -14,14 +14,14 @@ test_that("creation of rl_map from CellPhoneDB v4 input", { }) test_that("formating of SCENIC regulons output as a list", { - # use regulon list created in domino2 v0.2.1 + # use regulon list created in dominoSignal v0.2.1 regulon_ls <- create_regulon_list_scenic(regulons = v0.2.1$regulons_tiny) expect_equal(regulon_ls, v0.2.1$regulon_list_tiny) }) test_that("creation of a domino object from SCENIC and CellPhoneDB inputs", { - # domino object created in domino2 v0.2.1 - # rl_map created in domino2 v0.2.1 from CellPhoneDB v4 + # domino object created in dominoSignal v0.2.1 + # rl_map created in dominoSignal v0.2.1 from CellPhoneDB v4 # scenic inputs from pySCENIC v0.11.0 # minimal expression data from 360 cells in 3 cell types, # expression features for 16 genes @@ -45,8 +45,8 @@ test_that("creation of a domino object from SCENIC and CellPhoneDB inputs", { }) test_that("building a domino object under set parameters", { - # built domino object created in domino2 v0.2.1 - # domino object created in domino2 v0.2.1 + # built domino object created in dominoSignal v0.2.1 + # domino object created in dominoSignal v0.2.1 pbmc_dom_built <- build_domino( dom = v0.2.1$pbmc_dom_tiny, min_tf_pval = .05, diff --git a/vignettes/dominoSignal.Rmd b/vignettes/dominoSignal.Rmd index b606497..acd6b68 100644 --- a/vignettes/dominoSignal.Rmd +++ b/vignettes/dominoSignal.Rmd @@ -83,13 +83,14 @@ pbmc <- readRDS(pbmc) ## Installation -Installation of dominoSignal from Github can be achieved using the `{remotes}` package. +Installation of dominoSignal from Bioconductor can be achieved using the `{BiocManager}` package. -```{r, eval = FALSE} -if(!require(remotes)){ - install.packages("remotes") +```{r, eval=FALSE} +if (!require("BiocManager", quietly = TRUE)){ + install.packages("BiocManager") } -remotes::install_github("FertigLab/dominoSignal") + +BiocManager::install("dominoSignal") ``` ## Loading TF and R - L data