added citation

HectorRDB · Mar 31, 2021 · 6c4e6b0 · 6c4e6b0
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,7 +2,6 @@ Package: condiments
 Type: Package
 Title: Differential Topology, Progression and Differentiation
 Version: 0.99.12
-Date: 2020-09-17
 Authors@R: c(person("Hector", "Roux de Bezieux", role = c("aut", "cre"),
                      email = "hector.rouxdebezieux@berkeley.edu",
 		     comment = c(ORCID = "0000-0002-1489-8339")),
@@ -11,9 +10,8 @@ Authors@R: c(person("Hector", "Roux de Bezieux", role = c("aut", "cre"),
 Description: This package encapsulate many functions to conduct a differential topology analysis. It focuses on analyzing an 'omic dataset with multiple conditions. While the package is mostly geared toward scRNASeq, it does not place any restriction on the actual input format.
 License: MIT + file LICENSE
 Encoding: UTF-8
-LazyData: false
 URL: https://hectorrdb.github.io/condiments/index.html
-Depends: R (>= 4.1)
+Depends: R (>= 4.0)
 VignetteBuilder: knitr
 biocViews:
     RNASeq,

diff --git a/NEWS b/NEWS
@@ -1 +1,2 @@
-# Package Creation
+Changes in version 0.99.0 (2021-03-01)
++ Submitted to Bioconductor
diff --git a/R/differentiationTest.R b/R/differentiationTest.R
@@ -142,8 +142,8 @@ setMethod(f = "differentiationTest",
             }
             if (dplyr::n_distinct(conditions) > 2 && method != "Classifier") {
               method <- "Classifier"
-              warning(paste0("If more than two conditions are present, ",
-                             "only the Classifier method is possible."))
+              warning("If more than two conditions are present, ",
+                      "only the Classifier method is possible.")
             }
             res <- .differentiationTest(ws = cellWeights, conditions = conditions,
                                         global = global, pairwise = pairwise,
@@ -171,8 +171,8 @@ setMethod(f = "differentiationTest",
             }
             if (dplyr::n_distinct(conditions) > 2 && method != "Classifier") {
               method <- "Classifier"
-              warning(paste0("If more than two conditions are present, ",
-                             "only the Classifier method is possible."))
+              warning("If more than two conditions are present, ",
+                      "only the Classifier method is possible.")
             }
             if (slingParams(cellWeights)$reweight | slingParams(cellWeights)$reassign) {
               ws <- slingshot::slingCurveWeights(cellWeights, as.probs = TRUE)

diff --git a/R/progressionTest.R b/R/progressionTest.R
@@ -202,8 +202,8 @@ setMethod(f = "progressionTest",
               stop("Method must be one of KS, Classifier, mmd or permutation")
             }
             if (n_distinct(conditions) > 2 && method != "Classifier") {
-              warning(paste0("Changing to method classifier since more than ",
-                             "two conditions are present."))
+              warning("Changing to method classifier since more than ",
+                      "two conditions are present.")
               method <- "Classifier"
             }
             res <- .progressionTest(pst = pseudotime, ws = cellWeights,
@@ -229,8 +229,8 @@ setMethod(f = "progressionTest",
               stop("Method must be one of KS, Classifier, mmd or permutation")
             }
             if (n_distinct(conditions) > 2 && method != "Classifier") {
-              warning(paste0("Changing to method classifier since more than ",
-                             "two conditions are present."))
+              warning("Changing to method classifier since more than ",
+                      "two conditions are present.")
               method <- "Classifier"
             }
             pst <- slingshot::slingPseudotime(pseudotime, na = FALSE)

diff --git a/R/topologyTest.R b/R/topologyTest.R
@@ -228,8 +228,8 @@ setMethod(f = "topologyTest",
                                 args_wass = list(),
                                 nmax = nrow(slingshot::slingPseudotime(sds))){
             if (n_distinct(conditions) > 2 && methods != "Classifier") {
-              warning(paste0("Changing to methods `classifier` since more than ",
-                             "two conditions are present."))
+              warning("Changing to methods `classifier` since more than ",
+                      "two conditions are present.")
               methods <- "Classifier"
             }
             res <- .topologyTest(sds = sds,

diff --git a/README.md b/README.md
@@ -10,9 +10,21 @@
 
 ## Installation
 
+You can install the `condiments` from the devel branch of [bioconductor](https://www.bioconductor.org/packages/devel/bioc/html/condiments.html) using
+
+```r
+if(!requireNamespace("BiocManager", quietly = TRUE)) {
+ install.packages("BiocManager") 
+}
+BiocManager::install("tradeSeq")
+```
+
 To install the development version in `R`, run 
 
 ```r
+if(!requireNamespace("devtools", quietly = TRUE)) {
+ install.packages("devtools") 
+}
 devtools::install_github("HectorRDB/condiments")
 ```
 

diff --git a/inst/CITATION b/inst/CITATION
@@ -0,0 +1,16 @@
+citHeader("To cite Dune in publications use:")
+
+citEntry(
+  entry = "Article",
+  title = "Trajectory inference across multiple conditions with condiments: differential topology, progression, differentiation, and expression",
+  author = "Hector Roux de Bezieux and Koen Van den Berge and Kelly Street and Sandrine Dudoit",
+  year = "2021",
+	doi = "10.1101/2021.03.09.433671",
+	publisher = "Cold Spring Harbor Laboratory",
+	URL = "https://www.biorxiv.org/content/10.1101/2021.03.09.433671v1",
+	eprint = "https://www.biorxiv.org/content/10.1101/2021.03.09.433671v1.full.pdf",
+	journal = "bioRxiv",
+  textVersion = paste(
+
+  )
+)