Package: segmenter 1.11.0

Mahmoud Ahmed

segmenter: Perform Chromatin Segmentation Analysis in R by Calling ChromHMM

Chromatin segmentation analysis transforms ChIP-seq data into signals over the genome. The latter represents the observed states in a multivariate Markov model to predict the chromatin's underlying states. ChromHMM, written in Java, integrates histone modification datasets to learn the chromatin states de-novo. The goal of this package is to call chromHMM from within R, capture the output files in an S4 object and interface to other relevant Bioconductor analysis tools. In addition, segmenter provides functions to test, select and visualize the output of the segmentation.

Authors:Mahmoud Ahmed [aut, cre]

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segmenter.pdf |segmenter.html✨
segmenter/json (API)
NEWS

# Install 'segmenter' in R:
install.packages('segmenter', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/mahshaaban/segmenter/issues

Datasets:
  • test_obj - A segmentation object generated from the test data
  • test_objs - A a list of segmentation objects generated from the test data

On BioConductor:segmenter-1.11.0(bioc 3.20)segmenter-1.10.0(bioc 3.19)

bioconductor-package

39 exports 0.82 score 156 dependencies 1 mentions

Last updated 2 months agofrom:f47ee7cdb3

Exports:annotate_segmentsbinarize_bambinarize_bedbinscellscompare_modelscountsemissionemissions_fileenrichment_filesget_frequencyget_widthlearn_modellikelihoodmarkersmodelmodel_fileoverlapoverlap_filesplot_heatmapread_bam_fileread_bins_fileread_cellmark_fileread_chromsize_fileread_emissions_fileread_enrichment_fileread_model_fileread_overlap_fileread_segements_fileread_transitions_filesegmentsegments_filesshowstatesTEStidy_rangestransitiontransitions_fileTSS

Dependencies:abindAnnotationDbiapeaplotaskpassbamsignalsBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobbootcachemcaToolsChIPseekerchromhmmDatacirclizecliclueclustercodetoolscolorspaceComplexHeatmapcowplotcpp11crayoncurldata.tableDBIDelayedArraydigestdoParallelDOSEdplyrenrichplotfansifarverfastmapfastmatchfgseaforeachformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGetoptLongggforceggfunggnewscaleggplot2ggplotifyggraphggrepelggtreeGlobalOptionsglueGO.dbGOSemSimgplotsgraphlayoutsgridExtragridGraphicsgtablegtoolsHDO.dbhttrigraphIRangesisobanditeratorsjsonliteKEGGRESTKernSmoothlabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpatchworkpillarpkgconfigplogrplotrixplyrpngpolyclippurrrqvalueR6RColorBrewerRcppRcppArmadilloRcppEigenRCurlreshape2restfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscalesscatterpieshadowtextshapesnowSparseArraystringistringrSummarizedExperimentsyssystemfontstibbletidygraphtidyrtidyselecttidytreetreeiotweenrTxDb.Hsapiens.UCSC.hg19.knownGeneUCSC.utilsutf8vctrsviridisviridisLitewithrXMLXVectoryamlyulab.utilszlibbioc

Chromatin Segmentation Analysis Using segmenter

Rendered fromsegmenter.Rmdusingknitr::rmarkdownon Jul 01 2024.

Last update: 2021-06-09
Started: 2021-04-19

Readme and manuals

Help Manual

Help pageTopics
Call Java 'BinarizeBed'.Binarize
Call Java 'LearnModel'.LearnModel
Accessors for the 'segmentation' objectsaccessors bins bins,segmentation-method cells cells,segmentation-method counts counts,segmentation-method emission emission,segmentation-method likelihood likelihood,segmentation-method markers markers,segmentation-method model model,segmentation-method overlap overlap,segmentation-method segment segment,segmentation-method states states,segmentation-method TES TES,segmentation-method transition transition,segmentation-method TSS TSS,segmentation-method
Annotate segmentsannotate_segments
Binarize the bam filesbinarize_bam
Binarize the bed filesbinarize_bed
Compare two or more modelscompare_models
Count reads in 'GRanges' objects from bam filescount_reads_ranges
Make emissions file nameemissions_file
Make enrichment file namesenrichment_files
Get the frequency of the segments in each cell typeget_frequency
Get the width of the segments in each cell typeget_width
Learn a multi-state model from chromatin datalearn_model
Merge segments and bins objectsmerge_segments_bins
Methods to interact with 'segmentation' objectsmethods show,segmentation-method
Make model file namemodel_file
Make overlap file namesoverlap_files
Visualize the model outputplot_heatmap
Format the loaded binarized datarange_bins
Format the loaded counts datarange_counts
Read 'bam' filesread_bam_file
Read 'bins' filesread_bins_file
Read 'cellmarktable' fileread_cellmark_file
Read 'chromsizefile'read_chromsize_file
Read 'emissions' fileread_emissions_file
Read 'enrichment' filesread_enrichment_file
Read 'modelfile'read_model_file
Read 'segments' filesread_overlap_file
Read 'segments' filesread_segements_file
Read 'transitions' fileread_transitions_file
segmentation objectsclass:segmentation segmentation segmentation-class
Make segments file namessegments_files
A segmentation object generated from the test datatest_obj
A a list of segmentation objects generated from the test datatest_objs
Tidy the metadata of a 'GRanges' objecttidy_ranges
Make transitions file nametransitions_file