1)https://www.bioconductor.org/packages/3.3/bioc/vignettes/ENCODExplorer/inst/doc/ENCODExplorer.html
New portal of ENCODE https://www.encodeproject.org/
#Load the ENCODExplorer
suppressMessages(library(ENCODExplorer))
#Find all the files from the experiment with biosample from A549 human cell using H2AFZ as antibody target
query_results <- searchEncode("a549 chip-seq homo sapiens h2afz") or
search_results <- searchEncode(searchTerm = "a549 chip-seq h2afz", limit = "all")
//downloadEncode(resultSet = search_results, resultOrigin = "searchEncode", format = "bed_broadPeak")
cant find any broadpeak files

2)Connect to an Oracle database(Encode sql Database) using R
http://rprogramming.net/connect-to-database-in-r/
channel <- odbcConnect("genome-mysql.cse.ucsc.edu", uid="genomep", pwd="password", believeNRows=FALSE)
http://stackoverflow.com/questions/15420999/rodbc-odbcdriverconnect-connection-error
#Database schema
install.packages("RMySQL")
library(RMySQL)
drv = dbDriver("MySQL")
con = dbConnect(drv,host="genome-mysql.cse.ucsc.edu",user="genomep",pass="password")
album = dbGetQuery(con,statement="show tables")
Tables_in_hgcentral
1          blatServers
2                clade
3                 dbDb
4             dbDbArch
5            defaultDb
6               gbNode
7          genomeClade
8            geoIpNode
9            hubPublic
10           jorgetest
11       liftOverChain
12       liftOver_bkup
13           sessionDb
14   tableDescriptions
15            targetDb
16              userDb
17           wikiTrack
3)Not working-->https://www.simple-talk.com/sql/reporting-services/making-data-analytics-simpler-sql-server-and-r/