Package: DMCFB 1.19.0
Farhad Shokoohi
DMCFB: Differentially Methylated Cytosines via a Bayesian Functional Approach
DMCFB is a pipeline for identifying differentially methylated cytosines using a Bayesian functional regression model in bisulfite sequencing data. By using a functional regression data model, it tries to capture position-specific, group-specific and other covariates-specific methylation patterns as well as spatial correlation patterns and unknown underlying models of methylation data. It is robust and flexible with respect to the true underlying models and inclusion of any covariates, and the missing values are imputed using spatial correlation between positions and samples. A Bayesian approach is adopted for estimation and inference in the proposed method.
Authors:
DMCFB_1.19.0.tar.gz
DMCFB_1.19.0.zip(r-4.5)DMCFB_1.19.0.zip(r-4.4)DMCFB_1.19.0.zip(r-4.3)
DMCFB_1.19.0.tgz(r-4.4-any)DMCFB_1.19.0.tgz(r-4.3-any)
DMCFB_1.19.0.tar.gz(r-4.5-noble)DMCFB_1.19.0.tar.gz(r-4.4-noble)
DMCFB_1.19.0.tgz(r-4.4-emscripten)DMCFB_1.19.0.tgz(r-4.3-emscripten)
DMCFB.pdf |DMCFB.html✨
DMCFB/json (API)
NEWS
| # Install 'DMCFB' in R: |
| install.packages('DMCFB', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/shokoohi/dmcfb/issues
On BioConductor:DMCFB-1.19.0(bioc 3.20)DMCFB-1.18.0(bioc 3.19)
Last updated 2 months agofrom:32e9c21e68
Exports:cBSDMCcombinefindDMCFBmethLevelsmethLevels<-methReadsmethReads<-plotDMCFBreadBismarktotalReadstotalReads<-
Dependencies:abindarmaskpassbenchmarkmebenchmarkmeDataBHbiglmBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopsbootclicodacodetoolscpp11crayoncurldata.tableDBIDelayedArraydoParalleldplyrfansifastDummiesforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesgluehttrIRangesiteratorsjsonlitelambda.rlatticelifecyclelme4magrittrMASSMatrixMatrixGenericsmatrixStatsmimeminqanlmenloptropensslpillarpkgconfigR6RcppRcppEigenRCurlrestfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorssnowSparseArrayspeedglmstringistringrSummarizedExperimentsystibbletidyselectUCSC.utilsutf8vctrswithrXMLXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Differentially Methylated cytosines using functional Bayesian regression models | DMCFB-package DMCFB |
| BSDMC object | BSDMC BSDMC-class |
| cBSDMC method | cBSDMC cBSDMC,matrix,matrix,matrix,GRanges-method cBSDMC-method |
| combine method | combine combine,BSDMC,BSDMC-method combine-method |
| findDMCFB method | findDMCFB findDMCFB,BSDMC-method findDMCFB-method |
| methLevels method | methLevels methLevels,BSDMC-method methLevels-method methLevels<- methLevels<-,BSDMC,matrix-method |
| methReads method | methReads methReads,BSDMC-method methReads-method methReads<- methReads<-,BSDMC,matrix-method |
| params | params |
| plotDMCFB method | plotDMCFB plotDMCFB,BSDMC-method plotDMCFB-method |
| readBismark method | readBismark readBismark,character,character,numeric-method readBismark,character,data.frame,numeric-method readBismark,character,DataFrame,numeric-method readBismark-method |
| totalReads method | totalReads totalReads,BSDMC-method totalReads-method totalReads<- totalReads<-,BSDMC,matrix-method |
