Aadd yarn (#314)

* update documentation

* remove monster tests

* reduce monstr test

* update documentation

* remove diffedge example

* reduce monster tests

* remove spider example

* update monster examples

* remove lioness tests

* remove pada tests

* add citation

* add yarn

* add yarn

* add yarn

* change yarn vignette

* change yarn vignette

* change yarn vignette

* add download data set

* add download data set

* update yarn

* update yarn

* update yarn

* update yarn

* add download file

* add download file

* add download file

* update workflow

* update workflow

* update to R 4.3

* update to R 4.3

.github/workflows/main.yml

@@ -30,7 +30,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest]
-        r-version: [4.2]
+        r-version: [4.3]
 
     steps:
 

.gitignore

@@ -34,3 +34,5 @@ tests/testthat/*.vcf
 vignettes/*.npy
 docs/*.npy
 docs/reference/*.npy
+bladder.rdata
+skin.rdata

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: netZooR
 Type: Package
 Title: Unified methods for the inference and analysis of gene regulatory networks
-Version: 1.5.6
-Date: 2024-02-02
+Version: 1.5.17
+Date: 2024-02-29
 Authors@R: c(person("Marouen", "Ben Guebila",
 			email = "benguebila@hsph.harvard.edu", role = c("aut","cre"), comment = c(ORCID = "0000-0001-5934-966X")),
 	     person("Tian", "Wang", 
@@ -22,11 +22,11 @@ Authors@R: c(person("Marouen", "Ben Guebila",
 Maintainer: Marouen Ben Guebila <marouen.b.guebila@gmail.com>
 Description: netZooR unifies the implementations of several Network Zoo methods (netzoo, netzoo.github.io) into a single package by creating interfaces between network inference and network analysis methods. Currently, the package has 3 methods for network inference including PANDA and its optimized implementation OTTER (network reconstruction using mutliple lines of biological evidence), LIONESS (single-sample network inference), and EGRET (genotype-specific networks). Network analysis methods include CONDOR (community detection), ALPACA (differential community detection), CRANE (significance estimation of differential modules), MONSTER (estimation of network transition states). In addition, YARN allows to process gene expresssion data for tissue-specific analyses and SAMBAR infers missing mutation data based on pathway information.
 Depends: R (>= 4.2.0),
-   	 igraph,
+   igraph,
 	 reticulate,
-         yarn,
 	 pandaR,
-         matrixcalc
+   matrixcalc,
+   Biobase
 Remotes: 
 	 stan-dev/cmdstanr,
 	 jnpaulson/pandaR, 
@@ -75,7 +75,15 @@ Imports:
     GeneNet,
     loo,
     rARPACK,
-    corpcor
+    corpcor,
+    biomaRt,
+    downloader,
+    edgeR,
+    limma,
+    preprocessCore,
+    readr,
+    RColorBrewer,
+    quantro
 License: GPL-3
 Encoding: UTF-8
 LazyData: false

NAMESPACE

@@ -5,6 +5,9 @@ export(adj2regulon)
 export(alpaca)
 export(alpacaCrane)
 export(alpacaExtractTopGenes)
+export(annotateFromBiomart)
+export(checkMisAnnotation)
+export(checkTissuesToMerge)
 export(cobra)
 export(condorCluster)
 export(condorCoreEnrich)
@@ -17,10 +20,15 @@ export(craneBipartite)
 export(craneUnipartite)
 export(createCondorObject)
 export(createPandaStyle)
+export(downloadGTEx)
 export(dragon)
 export(el2adj)
 export(el2regulon)
 export(elistToAdjMat)
+export(filterGenes)
+export(filterLowGenes)
+export(filterMissingGenes)
+export(filterSamples)
 export(lioness)
 export(lionessPy)
 export(monster)
@@ -36,11 +44,15 @@ export(monsterTransformationMatrix)
 export(monsterTransitionNetworkPlot)
 export(monsterTransitionPCAPlot)
 export(monsterdTFIPlot)
+export(normalizeTissueAware)
 export(otter)
 export(pandaDiffEdges)
 export(pandaPy)
 export(pandaToAlpaca)
 export(pandaToCondorObject)
+export(plotCMDS)
+export(plotDensity)
+export(plotHeatmap)
 export(priorPp)
 export(puma)
 export(runEgret)
@@ -73,12 +85,33 @@ import(reticulate)
 import(stats, except= c(cov2cor,decompose,toeplitz,lowess,update,spectrum))
 import(vegan, except=diversity)
 import(viridisLite)
-import(yarn)
+importClassesFrom(Biobase,ExpressionSet)
+importClassesFrom(Biobase,eSet)
+importFrom(Biobase,"assayData<-")
+importFrom(Biobase,"fData<-")
+importFrom(Biobase,"pData<-")
+importFrom(Biobase,"phenoData<-")
+importFrom(Biobase,"storageMode<-")
+importFrom(Biobase,AnnotatedDataFrame)
+importFrom(Biobase,ExpressionSet)
 importFrom(Biobase,assayData)
+importFrom(Biobase,exprs)
+importFrom(Biobase,fData)
+importFrom(Biobase,featureNames)
+importFrom(Biobase,pData)
+importFrom(Biobase,storageMode)
+importFrom(RColorBrewer,brewer.pal)
 importFrom(assertthat,assert_that)
+importFrom(biomaRt,getBM)
+importFrom(biomaRt,useMart)
+importFrom(downloader,download)
+importFrom(edgeR,cpm)
+importFrom(gplots,heatmap.2)
+importFrom(graphics,abline)
 importFrom(graphics,axis)
 importFrom(graphics,box)
 importFrom(graphics,hist)
+importFrom(graphics,legend)
 importFrom(graphics,mtext)
 importFrom(graphics,par)
 importFrom(graphics,plot)
@@ -90,6 +123,7 @@ importFrom(igraph,E)
 importFrom(igraph,V)
 importFrom(igraph,graph.data.frame)
 importFrom(igraph,plot.igraph)
+importFrom(limma,normalizeQuantiles)
 importFrom(matrixStats,colSds)
 importFrom(matrixStats,rowSds)
 importFrom(methods,is)
@@ -99,8 +133,18 @@ importFrom(parallel,mclapply)
 importFrom(penalized,optL1)
 importFrom(penalized,penalized)
 importFrom(penalized,predict)
+importFrom(preprocessCore,normalize.quantiles)
+importFrom(quantro,matdensity)
+importFrom(readr,problems)
+importFrom(readr,read_tsv)
 importFrom(reshape,melt.array)
 importFrom(reshape2,dcast)
 importFrom(reshape2,melt)
+importFrom(stats,ave)
+importFrom(stats,cmdscale)
+importFrom(stats,dist)
+importFrom(stats,model.matrix)
+importFrom(stats,runmed)
+importFrom(stats,sd)
 importFrom(tidyr,spread)
 importFrom(utils,write.table)

R/ALPACA.R

@@ -16,7 +16,6 @@
 #' @importFrom utils write.table
 #' @rawNamespace import(GOstats, except= makeGOGraph)
 #' @import org.Hs.eg.db
-#' @import yarn 
 #' @export
 #'