Package: PICS 2.51.0

Renan Sauteraud

PICS: Probabilistic inference of ChIP-seq

Probabilistic inference of ChIP-Seq using an empirical Bayes mixture model approach.

Authors:Xuekui Zhang <[email protected]>, Raphael Gottardo <[email protected]>

PICS_2.51.0.tar.gz
PICS_2.51.0.zip(r-4.5)PICS_2.51.0.zip(r-4.4)PICS_2.51.0.zip(r-4.3)
PICS_2.51.0.tgz(r-4.4-x86_64)PICS_2.51.0.tgz(r-4.4-arm64)PICS_2.51.0.tgz(r-4.3-x86_64)PICS_2.51.0.tgz(r-4.3-arm64)
PICS_2.51.0.tar.gz(r-4.5-noble)PICS_2.51.0.tar.gz(r-4.4-noble)
PICS_2.51.0.tgz(r-4.4-emscripten)PICS_2.51.0.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

Uses libs:

gsl– GNU Scientific Library (GSL)

On BioConductor:PICS-2.51.0(bioc 3.21)PICS-2.50.0(bioc 3.20)

clustering visualization sequencing chipseq

6.26 score 1 packages 7 scripts 310 downloads 73 mentions 35 exports 42 dependencies

Last updated 23 days agofrom:59be92f64b. Checks:OK: 4 WARNING: 4 NOTE: 1. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 31 2024
R-4.5-win-x86_64	NOTE	Oct 31 2024
R-4.5-linux-x86_64	OK	Oct 31 2024
R-4.4-win-x86_64	OK	Oct 31 2024
R-4.4-mac-x86_64	WARNING	Oct 31 2024
R-4.4-mac-aarch64	WARNING	Oct 31 2024
R-4.3-win-x86_64	OK	Oct 31 2024
R-4.3-mac-x86_64	WARNING	Oct 31 2024
R-4.3-mac-aarch64	WARNING	Oct 31 2024

Exports:bam2gr candidate.region chromosome code delta K makeGRangesOutput map maxRange minRange mu PICS picsFDR plot score scoreForward scoreReverse se seF segChrRead segmentPICS segReads segReadsGeneric segReadsList segReadsListPE segReadsPE seR setParaEM setParaPrior show sigmaSqF sigmaSqR summary summarySeg w

Dependencies:abind askpass BH Biobase BiocGenerics BiocParallel Biostrings bitops codetools cpp11 crayon curl DelayedArray formatR futile.logger futile.options GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges httr IRanges jsonlite lambda.r lattice Matrix MatrixGenerics matrixStats mime openssl R6 Rhtslib Rsamtools S4Arrays S4Vectors snow SparseArray SummarizedExperiment sys UCSC.utils XVector zlibbioc

PICS: Probabilistic Inference for ChIP-Seq

Renan Sauteraud

Rendered fromPICS.Rmdusingknitr::knitron Oct 31 2024.

Last update: 2020-01-15
Started: 2019-11-08

Citation

Development and contributors

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