Package: PICS 2.49.0
Renan Sauteraud
PICS: Probabilistic inference of ChIP-seq
Probabilistic inference of ChIP-Seq using an empirical Bayes mixture model approach.
Authors:
PICS_2.49.0.tar.gz
PICS_2.49.0.zip(r-4.5)PICS_2.49.0.zip(r-4.4)PICS_2.49.0.zip(r-4.3)
PICS_2.49.0.tgz(r-4.4-arm64)PICS_2.49.0.tgz(r-4.4-x86_64)PICS_2.49.0.tgz(r-4.3-arm64)PICS_2.49.0.tgz(r-4.3-x86_64)
PICS_2.49.0.tar.gz(r-4.5-noble)PICS_2.49.0.tar.gz(r-4.4-noble)
PICS_2.49.0.tgz(r-4.4-emscripten)PICS_2.49.0.tgz(r-4.3-emscripten)
PICS.pdf |PICS.html✨
PICS/json (API)
| # Install 'PICS' in R: |
| install.packages('PICS', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/srenan/pics/issues
On BioConductor:PICS-2.49.0(bioc 3.20)PICS-2.48.0(bioc 3.19)
Last updated 2 months agofrom:5328ba57b2
Exports:bam2grcandidate.regionchromosomecodedeltaKmakeGRangesOutputmapmaxRangeminRangemuPICSpicsFDRplotscorescoreForwardscoreReverseseseFsegChrReadsegmentPICSsegReadssegReadsGenericsegReadsListsegReadsListPEsegReadsPEseRsetParaEMsetParaPriorshowsigmaSqFsigmaSqRsummarysummarySegw
Dependencies:abindaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitopscodetoolscpp11crayoncurlDelayedArrayformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangeshttrIRangesjsonlitelambda.rlatticeMatrixMatrixGenericsmatrixStatsmimeopensslR6RhtslibRsamtoolsS4ArraysS4VectorssnowSparseArraySummarizedExperimentsysUCSC.utilsXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Pre-process bam files | bam2gr |
| Identify candidate regions | candidate.region |
| Export a PICS object to GRanges | makeGRangesOutput |
| Estimation of binding site positions | PICS |
| PICS class | chromosome,pics-method code,pics-method delta,pics-method K,pics-method maxRange,pics-method minRange,pics-method mu,pics-method pics-class score,pics-method scoreForward,pics-method scoreReverse,pics-method se,pics-method seF,pics-method seR,pics-method show,pics-method sigmaSqF,pics-method sigmaSqR,pics-method summary,pics-method w,pics-method |
| Generics associated with pics classes | chromosome chromosome,data.frame-method code delta delta,data.frame-method K maxRange minRange mu mu,data.frame-method pics-generics score score,data.frame-method scoreForward scoreForward,data.frame-method scoreReverse scoreReverse,data.frame-method se se,data.frame-method seF seF,data.frame-method seR seR,data.frame-method sigmaSqF sigmaSqF,data.frame-method sigmaSqR sigmaSqR,data.frame-method w |
| picsError class | chromosome,picsError-method code,picsError-method delta,picsError-method K,picsError-method maxRange,picsError-method minRange,picsError-method mu,picsError-method picsError-class score,picsError-method scoreForward,picsError-method scoreReverse,picsError-method se,picsError-method seF,picsError-method seR,picsError-method show,picsError-method sigmaSqF,picsError-method sigmaSqR,picsError-method w,picsError-method |
| Estimate the FDR | picsFDR |
| List of PICS objects | chromosome,picsList-method code,picsList-method delta,picsList-method K,picsList-method length,picsList-method maxRange,picsList-method minRange,picsList-method mu,picsList-method picsList-class score,picsList-method scoreForward,picsList-method scoreReverse,picsList-method se,picsList-method seF,picsList-method seR,picsList-method show,picsList-method sigmaSqF,picsList-method sigmaSqR,picsList-method summary,picsList-method w,picsList-method [,picsList,ANY,ANY,ANY-method [[,picsList,ANY,ANY-method |
| Plot PICS FDR | plot,picsList,picsList-method plot-FDR |
| Plot methods for PICS objects | plot,pics,segReads-method plot,picsError,segReads-method plot,picsList,segReadsList-method plot-pics |
| Segmentation of paired-end sequencing data | segChrRead |
| Segment the genome into candidate regions | segmentPICS |
| Classes and functions to segment the genome in candidate regions | length,segReadsList-method map map,segReads-method map,segReadsList-method segReads segReads-class segReadsList segReadsList-class show,segReads-method show,segReadsList-method summary,segReads-method summary,segReadsList-method [,segReadsList,ANY,ANY,ANY-method [[,segReadsList,ANY,ANY-method |
| Perform genome segmentation depending | segReadsGeneric |
| Class and methods for list of candidate regions from paired-end data | segReadsListPE segReadsListPE-class [,segReadsListPE,ANY,ANY,ANY-method [[,segReadsListPE,ANY,ANY-method |
| Classe and methods for candidate regions from paired-end data | segReadsPE segReadsPE-class |
| List of parameters for the EM algorithm that can be used as an argument of PICS. | setParaEM |
| List of parameters that can be used as an argument of PICS. | setParaPrior |
| Summarize segmentList objects | summarySeg |
