@@ -1,6 +1,6 @@

 Package: PanomiR

-Title: Inferring miRNAs targeting of pathway groups

-Version: 0.99.7

+Title: Detection of miRNAs that regulate interacting groups of pathways

+Version: 0.99.8

 Authors@R: c(

     person("Pourya", "Naderi", email = "pouryany@gmail.com",

            role = c("aut", "cre")),

@@ -14,8 +14,9 @@ Description: PanomiR is a package to detect miRNAs that target groups of

     pathways from gene expression data. This package provides functionality 

     for generating pathway activity profiles, determining differentially

     activated pathways between user-specified conditions, determining 

-    clusters of pathways via PCxN package, and generating miRNAs targeting

-    clusters of pathways. Each function can be used on its own.

+    clusters of pathways via the PCxN package, and generating miRNAs targeting

+    clusters of pathways. These function can be used separately or sequentially

+    to analyze RNA-Seq data.

 License: MIT + file LICENSE

 Encoding: UTF-8

 RoxygenNote: 7.1.2

@@ -1,7 +1,7 @@

 ---

 title: "README"

-author: "Pourya Naderi (Hide Lab)"

-date: "9/16/2021"

+author: "Pourya Naderi, Alan Teo, Ilya Sytchev, and Winston Hide"

+date: "`r format(Sys.Date(), '%m/%d/%Y')`"

 bibliography: vignettes/references.bib  

 output:

   md_document:

@@ -406,7 +406,7 @@ sessionInfo()

     ## R Under development (unstable) (2021-12-03 r81290)

     ## Platform: x86_64-apple-darwin17.0 (64-bit)

-    ## Running under: macOS Mojave 10.14.6

+    ## Running under: macOS Big Sur/Monterey 10.16

     ## 

     ## Matrix products: default

     ## BLAS:   /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib

@@ -419,7 +419,7 @@ sessionInfo()

     ## [1] stats     graphics  grDevices utils     datasets  methods   base     

     ## 

     ## other attached packages:

-    ## [1] PanomiR_0.99.1

+    ## [1] PanomiR_0.99.4

     ## 

     ## loaded via a namespace (and not attached):

     ##   [1] fgsea_1.21.0           colorspace_2.0-2       ggtree_3.3.1          

@@ -434,21 +434,21 @@ sessionInfo()

     ##  [28] httr_1.4.2             assertthat_0.2.1       Matrix_1.4-0          

     ##  [31] fastmap_1.1.0          lazyeval_0.2.2         cli_3.1.0             

     ##  [34] limma_3.51.2           tweenr_1.0.2           htmltools_0.5.2       

-    ##  [37] tools_4.2.0            igraph_1.2.10          gtable_0.3.0          

+    ##  [37] tools_4.2.0            igraph_1.2.11          gtable_0.3.0          

     ##  [40] glue_1.6.0             GenomeInfoDbData_1.2.7 reshape2_1.4.4        

     ##  [43] DO.db_2.9              dplyr_1.0.7            fastmatch_1.1-3       

     ##  [46] Rcpp_1.0.7             enrichplot_1.15.2      Biobase_2.55.0        

-    ##  [49] vctrs_0.3.8            Biostrings_2.63.0      ape_5.6               

+    ##  [49] vctrs_0.3.8            Biostrings_2.63.1      ape_5.6-1             

     ##  [52] nlme_3.1-153           ggraph_2.0.5           xfun_0.29             

     ##  [55] stringr_1.4.0          lifecycle_1.0.1        clusterProfiler_4.3.1 

-    ##  [58] XML_3.99-0.8           DOSE_3.21.1            org.Hs.eg.db_3.14.0   

+    ##  [58] XML_3.99-0.8           DOSE_3.21.2            org.Hs.eg.db_3.14.0   

     ##  [61] zlibbioc_1.41.0        MASS_7.3-54            scales_1.1.1          

     ##  [64] tidygraph_1.2.0        parallel_4.2.0         RColorBrewer_1.1-2    

     ##  [67] yaml_2.2.1             memoise_2.0.1          gridExtra_2.3         

     ##  [70] ggplot2_3.3.5          downloader_0.4         ggfun_0.0.4           

     ##  [73] yulab.utils_0.0.4      stringi_1.7.6          RSQLite_2.2.9         

-    ##  [76] S4Vectors_0.33.8       tidytree_0.3.6         BiocGenerics_0.41.2   

-    ##  [79] BiocParallel_1.29.8    GenomeInfoDb_1.31.1    rlang_0.4.12          

+    ##  [76] S4Vectors_0.33.9       tidytree_0.3.6         BiocGenerics_0.41.2   

+    ##  [79] BiocParallel_1.29.10   GenomeInfoDb_1.31.1    rlang_0.4.12          

     ##  [82] pkgconfig_2.0.3        bitops_1.0-7           evaluate_0.14         

     ##  [85] lattice_0.20-45        purrr_0.3.4            treeio_1.19.1         

     ##  [88] patchwork_1.1.1        shadowtext_0.1.0       bit_4.0.4             

@@ -1,7 +1,6 @@

 ---

-title: "PanomiR Package Vignette"

-author: "Pourya Naderi"

-package: PanomiR

+title: "miRNA and pathway analysis with PanomiR"

+author: "Pourya Naderi, Alan Teo, Ilya Sytchev, and Winston Hide"

 output: 

   BiocStyle::html_document

 bibliography: references.bib  

@@ -26,7 +25,7 @@ functionality in PanomiR.

 # Installation

-PanomiR can be accessed via Bioconductor. To install, start R (version >= 4.1.0)

+PanomiR can be accessed via Bioconductor. To install, start R (version >= 4.2.0)

 and run the following code.

 ```{r installation_bioc, eval = FALSE}