cinaR 0.2.4: Fix CRAN/update site

eonurk · May 22, 2024 · fb3fea4 · fb3fea4
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diff --git a/.gitignore b/.gitignore
@@ -40,3 +40,4 @@ cinaR.Rproj
 inst/doc
 
 pkgdown
+docs
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,12 +1,13 @@
 Package: cinaR
 Type: Package
 Title: A Computational Pipeline for Bulk 'ATAC-Seq' Profiles
-Version: 0.2.3
+Version: 0.2.4
 Authors@R: 
     c(person(given = "Onur",
              family = "Karakaslar",
              role = c("aut", "cre"),
-             email = "[email protected]"),
+             email = "[email protected]",
+             comment = c(ORCID = "0000-0002-9182-910X")),
       person(given = "Duygu",
              family = "Ucar",
              role = "aut",
@@ -23,15 +24,12 @@ URL: https://github.com/eonurk/cinaR/
 BugReports: https://github.com/eonurk/cinaR/issues/
 biocViews:
 Depends: R (>= 4.0.0)
-Imports: ChIPseeker, 
+Imports: BiocManager,
          DESeq2, 
          dplyr,
          edgeR, 
          fgsea,
          GenomicRanges, 
-         TxDb.Hsapiens.UCSC.hg38.knownGene, 
-         TxDb.Hsapiens.UCSC.hg19.knownGene, 
-         TxDb.Mmusculus.UCSC.mm10.knownGene,
          ggplot2,
          ggrepel,
          grDevices,
@@ -42,9 +40,12 @@ Imports: ChIPseeker,
          RColorBrewer,
          sva,
          writexl 
-RoxygenNote: 7.1.2
-Suggests: 
-    knitr,
-    rmarkdown,
-    markdown
+RoxygenNote: 7.2.3
+Suggests: ChIPseeker, 
+          knitr,
+          rmarkdown,
+          markdown,
+          TxDb.Hsapiens.UCSC.hg38.knownGene, 
+          TxDb.Hsapiens.UCSC.hg19.knownGene, 
+          TxDb.Mmusculus.UCSC.mm10.knownGene
 VignetteBuilder: knitr, rmarkdown, markdown
diff --git a/NAMESPACE b/NAMESPACE
@@ -14,5 +14,8 @@ export(run_enrichment)
 export(scale_rows)
 export(show_comparisons)
 export(verboseFn)
+importFrom(BiocManager,install)
 importFrom(edgeR,cpm)
 importFrom(edgeR,filterByExpr)
+importFrom(utils,install.packages)
+importFrom(utils,installed.packages)
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,11 @@
+# cinaR 0.2.4
+- Bug fix and changes:
+    - Bioconductor related packages are suggested
+    - Added .on_attach() for smooth CRAN checks 
+
+# cinaR 0.2.3
+- Minor improvements
+
 # cinaR 0.2.2
 * Added:
   - `comparison.scheme` either set to `OVO` (default) which will compare each contrasts to each other. If it's set to `OVA` each contrast will be compared to rest. 

diff --git a/R/zzz.R b/R/zzz.R
@@ -0,0 +1,26 @@
+#' @importFrom utils install.packages installed.packages
+#' @importFrom BiocManager install
+NULL
+
+# Function to check and install missing Bioconductor dependencies
+check_and_install_bioc_dependencies <- function() {
+    missing_pkgs <- c("ChIPseeker", "TxDb.Hsapiens.UCSC.hg38.knownGene", 
+                      "TxDb.Hsapiens.UCSC.hg19.knownGene", 
+                      "TxDb.Mmusculus.UCSC.mm10.knownGene")
+    installed <- utils::installed.packages()[, "Package"]
+    missing <- missing_pkgs[!(missing_pkgs %in% installed)]
+
+    if (length(missing)) {
+        message("Installing missing Bioconductor packages: ", paste(missing, collapse = ", "))
+        if (!requireNamespace("BiocManager", quietly = TRUE)) {
+            utils::install.packages("BiocManager")
+        }
+        BiocManager::install(missing)
+    } else {
+        message("All required Bioconductor packages are already installed.")
+    }
+}
+
+.onAttach <- function(libname, pkgname) {
+    packageStartupMessage("To ensure all required Bioconductor packages are installed, run: check_and_install_bioc_dependencies()")
+}
diff --git a/README.Rmd b/README.Rmd
@@ -41,9 +41,6 @@ To get bug fix and use a feature from the development version:
 # install.packages("devtools")
 devtools::install_github("eonurk/cinaR")
 ```
-## Usage
-
-For more details please go to our site from [here!](https://eonurk.github.io/cinaR/articles/cinaR.html)
 
 ### Known Installation Issues
 
@@ -54,14 +51,45 @@ Therefore, you may need to install them manually:
 BiocManager::install(c("ChIPseeker", "DESeq2", "edgeR", "fgsea","GenomicRanges", "limma", "preprocessCore", "sva", "TxDb.Hsapiens.UCSC.hg38.knownGene", "TxDb.Hsapiens.UCSC.hg19.knownGene", "TxDb.Mmusculus.UCSC.mm10.knownGene"))
 ```
 
+## Usage
 
-## Contribution
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(dpi=300,fig.width=6)
+```
 
-You can send pull requests to make your contributions.
+```{r}
+library(cinaR)
+
+# create contrast vector which will be compared.
+contrasts<- c("B6", "B6", "B6", "B6", "B6", "NZO", "NZO", "NZO", "NZO", "NZO", "NZO", 
+              "B6", "B6", "B6", "B6", "B6", "NZO", "NZO", "NZO", "NZO", "NZO", "NZO")
 
-## Author
+# If reference genome is not set hg38 will be used!
+results <- cinaR(bed, contrasts, reference.genome = "mm10")
+
+pca_plot(results, contrasts, show.names = F)
+```
 
-- [E Onur Karakaslar](https://eonurk.github.io/)
+> For more details please go to our site from [here!](https://eonurk.github.io/cinaR/articles/cinaR.html)
+
+
+## Citation
+```
+@article {Karakaslar2021.03.05.434143,
+	author = {Karakaslar, E Onur and Ucar, Duygu},
+	title = {cinaR: A comprehensive R package for the differential analyses and 
+	functional interpretation of ATAC-seq data},
+	year = {2021},
+	doi = {10.1101/2021.03.05.434143},
+	publisher = {Cold Spring Harbor Laboratory},
+	URL = {https://www.biorxiv.org/content/early/2021/03/08/2021.03.05.434143.1},
+	journal = {bioRxiv}
+}
+```
+
+## Contribution
+
+You can send pull requests to make your contributions.
 
 ## License
 

diff --git a/README.md b/README.md
@@ -38,11 +38,6 @@ To get bug fix and use a feature from the development version:
 devtools::install_github("eonurk/cinaR")
 ```
 
-## Usage
-
-For more details please go to our site from
-[here!](https://eonurk.github.io/cinaR/articles/cinaR.html)
-
 ### Known Installation Issues
 
 Sometimes bioconductor related packages may not be installed
@@ -53,14 +48,63 @@ Therefore, you may need to install them manually:
 BiocManager::install(c("ChIPseeker", "DESeq2", "edgeR", "fgsea","GenomicRanges", "limma", "preprocessCore", "sva", "TxDb.Hsapiens.UCSC.hg38.knownGene", "TxDb.Hsapiens.UCSC.hg19.knownGene", "TxDb.Mmusculus.UCSC.mm10.knownGene"))
 ```
 
-## Contribution
+## Usage
 
-You can send pull requests to make your contributions.
+``` r
+library(cinaR)
+#> Checking for required Bioconductor packages...
+#> All required Bioconductor packages are already installed.
+
+# create contrast vector which will be compared.
+contrasts<- c("B6", "B6", "B6", "B6", "B6", "NZO", "NZO", "NZO", "NZO", "NZO", "NZO", 
+              "B6", "B6", "B6", "B6", "B6", "NZO", "NZO", "NZO", "NZO", "NZO", "NZO")
+
+# If reference genome is not set hg38 will be used!
+results <- cinaR(bed, contrasts, reference.genome = "mm10")
+#> >> Experiment type: ATAC-Seq
+#> >> Matrix is filtered!
+#> 
+#> >> preparing features information...      2024-05-22 09:51:42 
+#> >> identifying nearest features...        2024-05-22 09:51:42 
+#> >> calculating distance from peak to TSS...   2024-05-22 09:51:43 
+#> >> assigning genomic annotation...        2024-05-22 09:51:43 
+#> >> assigning chromosome lengths           2024-05-22 09:51:52 
+#> >> done...                    2024-05-22 09:51:52
+#> >> Method: edgeR
+#>  FDR:0.05& abs(logFC)<0
+#> >> Estimating dispersion...
+#> >> Fitting GLM...
+#> >> DA peaks are found!
+#> >> No `geneset` is specified so immune modules (Chaussabel, 2008) will be used!
+#> >> enrichment.method` is not selected. Hyper-geometric p-value (HPEA) will be used!
+#> >> Mice gene symbols are converted to human symbols!
+#> >> Enrichment results are ready...
+#> >> Done!
+
+pca_plot(results, contrasts, show.names = F)
+```
+
+<img src="man/figures/unnamed-chunk-5-1.png" width="100%" />
+
+> For more details please go to our site from
+> [here!](https://eonurk.github.io/cinaR/articles/cinaR.html)
+
+## Citation
 
-## Author
+    @article {Karakaslar2021.03.05.434143,
+        author = {Karakaslar, E Onur and Ucar, Duygu},
+        title = {cinaR: A comprehensive R package for the differential analyses and functional interpretation of ATAC-seq data},
+        year = {2021},
+        doi = {10.1101/2021.03.05.434143},
+        publisher = {Cold Spring Harbor Laboratory},
+        URL = {https://www.biorxiv.org/content/early/2021/03/08/2021.03.05.434143.1},
+        journal = {bioRxiv}
+    }
 
--   [E Onur Karakaslar](https://eonurk.github.io/)
+## Contribution
+
+You can send pull requests to make your contributions.
 
 ## License
 
--   GNU General Public License v3.0
+- GNU General Public License v3.0
diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -1,9 +1,8 @@
-destination: docs
+url: ~
 template:
-  params:
-    bootswatch: sandstone
-    ganalytics: UA-116646865-1
-
+  bootstrap: 5
+  bslib:
+    base_font: {google: "Open Sans"}
 authors:
   Onur Karakaslar:
     href: http://eonurk.github.io