Package: segmenter 1.19.0

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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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
segmenter/json (API)

# Install 'segmenter' in R:

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

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-1.19.0(bioc 3.24)segmenter-1.18.0(bioc 3.23)

software histonemodification bioconductor chromhmm segmentation-an

4.78 score 6 stars 9 scripts 319 downloads 1 mentions 39 exports 163 dependencies

Last updated from:da0c05d2e3. Checks:1 WARNING, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	280
linux-devel-x86_64	OK	634
source / vignettes	OK	682
linux-release-x86_64	OK	624
macos-release-arm64	OK	447
macos-oldrel-arm64	OK	398
windows-devel	OK	506
windows-release	OK	504
windows-oldrel	OK	498
wasm-release	OK	290

Exports:annotate_segments binarize_bam binarize_bed bins cells compare_models counts emission emissions_file enrichment_files get_frequency get_width learn_model likelihood markers model model_file overlap overlap_files plot_heatmap read_bam_file read_bins_file read_cellmark_file read_chromsize_file read_emissions_file read_enrichment_file read_model_file read_overlap_file read_segements_file read_transitions_file segment segments_files show states TES tidy_ranges transition transitions_file TSS

Dependencies:abind AnnotationDbi ape aplot askpass bamsignals base64enc BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob boot bslib cachem caTools ChIPseeker chromhmmData cigarillo circlize cli clue cluster codetools colorspace ComplexHeatmap cpp11 crayon curl DBI DelayedArray digest doParallel DOSE dplyr enrichit enrichplot evaluate farver fastmap fontawesome fontBitstreamVera fontLiberation fontquiver foreach formatR fs futile.logger futile.options gdtools generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GetoptLong ggforce ggfun ggiraph ggnewscale ggplot2 ggplotify ggrepel ggtangle ggtree GlobalOptions glue GO.db GOSemSim gplots gridGraphics gtable gtools highr htmltools htmlwidgets httr igraph IRanges isoband iterators jquerylib jsonlite KEGGREST KernSmooth knitr labeling lambda.r lattice lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mime nlme openssl patchwork pillar pkgconfig plotrix plyr png polyclip purrr R6 rappdirs RColorBrewer Rcpp RcppEigen RCurl reshape2 restfulr Rhtslib rjson rlang rmarkdown Rsamtools RSQLite rtracklayer S4Arrays S4Vectors S7 sass scales scatterpie Seqinfo shape snow SparseArray stringi stringr SummarizedExperiment sys systemfonts tibble tidydr tidyr tidyselect tidytree tinytex treeio tweenr TxDb.Hsapiens.UCSC.hg19.knownGene UCSC.utils utf8 vctrs viridisLite withr xfun XML XVector yaml yulab.utils

Chromatin Segmentation Analysis Using segmenter

Rendered fromsegmenter.Rmdusingknitr::rmarkdown

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

Help page	Topics
Call Java 'BinarizeBed'	.Binarize
Call Java 'LearnModel'	.LearnModel
Accessors for the 'segmentation' objects	accessors 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 segments	annotate_segments
Binarize the bam files	binarize_bam
Binarize the bed files	binarize_bed
Compare two or more models	compare_models
Count reads in 'GRanges' objects from bam files	count_reads_ranges
Make emissions file name	emissions_file
Make enrichment file names	enrichment_files
Get the frequency of the segments in each cell type	get_frequency
Get the width of the segments in each cell type	get_width
Learn a multi-state model from chromatin data	learn_model
Merge segments and bins objects	merge_segments_bins
Methods to interact with 'segmentation' objects	methods show,segmentation-method
Make model file name	model_file
Make overlap file names	overlap_files
Visualize the model output	plot_heatmap
Format the loaded binarized data	range_bins
Format the loaded counts data	range_counts
Read 'bam' files	read_bam_file
Read 'bins' files	read_bins_file
Read 'cellmarktable' file	read_cellmark_file
Read 'chromsizefile'	read_chromsize_file
Read 'emissions' file	read_emissions_file
Read 'enrichment' files	read_enrichment_file
Read 'modelfile'	read_model_file
Read 'segments' files	read_overlap_file
Read 'segments' files	read_segements_file
Read 'transitions' file	read_transitions_file
segmentation objects	class:segmentation segmentation segmentation-class
Make segments file names	segments_files
A segmentation object generated from the test data	test_obj
A a list of segmentation objects generated from the test data	test_objs
Tidy the metadata of a 'GRanges' object	tidy_ranges
Make transitions file name	transitions_file

Package: segmenter 1.19.0

segmenter: Perform Chromatin Segmentation Analysis in R by Calling ChromHMM

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