Update README.md, fixed formatting nearby devtools::install_git("https://git.psu.edu/genomath/MethylIT.git", branch = "v0.3.1.2")

Update README.md, added notes about how to install the version of MethylIT used for the paper: Heritable stress memory in plants involves methylome reprogramming of central, integrated environmental sensing and stress response networks, which goes like this: devtools::install_git("https://git.psu.edu/genomath/MethylIT.git", branch = "v0.3.1.2")

Add change from GRagesList to list, because GRagesList insists that all the column's names must have exactly the same name

merged new stuff from github including: M  MethylIT.Rproj M  NAMESPACE M  R/FisherTest.R M  R/countTest2.R M  R/estimateCutPoint.R M  R/findCutpoint.R M  R/getPotentialDIMP.R M  R/ggamma.R M  R/nonlinearFitDist.R M  R/rmstGR.R M  man/FisherTest.Rd M  man/countTest2.Rd M  man/findCutpoint.Rd M  man/ggamma.Rd M  man/rmstGR.Rd M  tests/testthat/test_GeneUpDownStream.R A  tests/testthat/test_predictProbDistr.R

Add new link to an example with simulated data

Add parallel computatio for Windows OS (via BiocParallel MulticoreParam bplapply SnowParam) in functions countTest2, estimateDivergence, and nonlinearFitDist

Add parallele computation to uniqueGRanges function in Windows, via BiocParallel bplapply SnowParam (hope!)