ettore, 0.32

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: scMuffin
 Title: MUlti-Features INtegrative approach for SC data analysis
-Version: 0.31
+Version: 0.32
 Date: 2022-04-19
 Authors@R: 
      c(person(given = "Noemi",
@@ -29,7 +29,7 @@ LazyData: true
 RoxygenNote: 7.1.2
 Encoding: UTF-8
 Depends: 
-    R (>= 3.5.0)
+    R (≥ 4.0.0)
 Imports:
     graphics,
     parallel,

vignettes/references.bib

@@ -1,3 +1,19 @@
+@article{Angerer2015,
+  title = {destiny: diffusion maps for large-scale single-cell data in R},
+  volume = {32},
+  number = {8},
+  url = {http://bioinformatics.oxfordjournals.org/content/32/8/1241},
+  doi = {10.1093/bioinformatics/btv715},
+  journal = {Bioinformatics},
+  author = {Philipp Angerer and Laleh Haghverdi and Maren Büttner and Fabian Theis and Carsten Marr and Florian Büttner},
+  pages = {1241},
+  pages = {1242},
+  pages = {1243},
+  organization = {Helmholtz-Zentrum München},
+  address = {Ingolstädter Landstraße 1, Neuherberg, Germany},
+  year = {2015},
+  note = {More information at },
+}
 @article{Yuan2018,
   author = {Yuan, Jinzhou and Levitin, Hanna Mendes and Frattini, Veronique and Bush, Erin C. and Boyett, Deborah M. and Samanamud, Jorge and Ceccarelli, Michele and Dovas, Athanassios and Zanazzi, George and Canoll, Peter and Bruce, Jeffrey N. and Lasorella, Anna and Iavarone, Antonio and Sims, Peter A.},
   doi = {10.1186/s13073-018-0567-9},

vignettes/scMuffin.Rmd

@@ -47,15 +47,43 @@ vignette: >
 knitr::include_graphics("images/scMuffin_logo_pontillism.jpg")
 ```
 
+## Dependencies
+To succesfully install scMUffin you need to install the following packages from Bioconductor (https://bioconductor.org):
+
+```{r, include=TRUE, eval=FALSE}
+if (!require("BiocManager", quietly = TRUE)){
+  install.packages("BiocManager")
+}
+BiocManager::install(c("org.Hs.eg.db", "destiny", "DESeq2", "BiocStyle"))
+```
+
+and the package destiny [@Angerer2015] from github:
+
+```{r, include=TRUE, eval=FALSE}
+if (!require("devtools", quietly = TRUE)){
+  install.packages("devtools")
+}
+devtools::install_github("theislab/destiny")
+```
+
+The other dependencies, if missing, should be automatically installed using the following commands:
+
+```{r, include=TRUE, eval=FALSE}
+devtools::install_github("emosca-cnr/scMuffin", build_vignettes = TRUE)
+```
+
+To load the packes and read this documentation:
+
 ```{r, include=TRUE, eval=FALSE}
-library(devtools)
-install_github("emosca-cnr/scMuffin", build_vignettes = TRUE)
 library(scMuffin)
+vignette("scMuffin")
 ```
 
-```{r, include=F, message=FALSE, warning=FALSE, eval=F}
+
+<!--```{r, include=F, message=FALSE, warning=FALSE, eval=F}
 devtools::load_all()
 ```
+-->
 
 # Obtaining the data used in this vignette
 To run the examples included in this vignette you need the following data: