Esempio n. 1
0
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)
Esempio n. 5
0
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')