def init_topGO(): try: topGO = importr("topGO") except: print ("It looks like topGO is not installed. Trying to install topGO via" "Bioconductor...") try: R.source("http://bioconductor.org/biocLite.R") R.biocLite("topGO") topGO = importr("topGO") except: print "Problem installing topGO from Bioconductor!" print ("Please install manually from: " "http://www.bioconductor.org/packages/2.13/bioc/html/topGO.html") return topGO
def init_qvalue(): global __qvalue if __qvalue is None: try: print "Importing qvalue ..." qvalue = importr("qvalue") except: print ("It looks like qvalue is not installed. Trying to install qvalue via" "Bioconductor...") try: R.source("http://bioconductor.org/biocLite.R") R.biocLite("qvalue") qvalue = importr("qvalue") except: print "Problem installing qvalue from Bioconductor!" print ("Please install manually from: " "http://www.bioconductor.org/packages/release/bioc/html/qvalue.html") __qvalue = qvalue
def init_topGO(): global __topGo if __topGo is None: try: print "Importing topGO ..." topGO = importr("topGO") except: print ("It looks like topGO is not installed. Trying to install topGO via" "Bioconductor...") try: R.source("http://bioconductor.org/biocLite.R") R.biocLite("topGO") topGO = importr("topGO") except: print "Problem installing topGO from Bioconductor!" print ("Please install manually from: " "http://www.bioconductor.org/packages/release/bioc/html/topGO.html") __topGo = topGO
def init_biomaRt(): global __biomaRt global __mart if __biomaRt is None: try: print "Importing biomaRt ..." biomaRt = importr("biomaRt") except: print ("It looks like biomaRt is not installed. Trying to install biomaRt via" "Bioconductor...") try: R.source("http://bioconductor.org/biocLite.R") R.biocLite("biomaRt") biomaRt = importr("biomaRt") except: print "Problem installing biomaRt from Bioconductor!" print ("Please install manually from: " "http://www.bioconductor.org/packages/release/bioc/html/biomaRt.html") __biomaRt = biomaRt __mart = R.useMart(biomart = "ensembl", dataset = __mart_dataset)
def run_cummeRbund_install(): """ provides R install of cummeRbund and provides user with all R output and prompts. """ r.source("http://bioconductor.org/biocLite.R") r.biocLite('cummeRbund')