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Mahmoud Ahmed
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Package: segmenter | ||
Type: Package | ||
Title: Perform Chromatin Segmentation Analysis in R by Calling ChromHMM | ||
Version: 0.99.0 | ||
Description: 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@R: person("Mahmoud", "Ahmed", | ||
email = "mahmoud.s.fahmy@students.kasralainy.edu.eg", | ||
role = c("aut", "cre"), | ||
comment = c(ORCID = "0000-0002-4377-6541")) | ||
License: GPL-3 | ||
Encoding: UTF-8 | ||
LazyData: true | ||
RoxygenNote: 7.1.1 | ||
Depends: R (>= 4.0) | ||
Suggests: | ||
testthat, | ||
knitr, | ||
rmarkdown, | ||
TxDb.Hsapiens.UCSC.hg18.knownGene, | ||
Gviz | ||
Imports: | ||
ChIPseeker, | ||
GenomicRanges, | ||
SummarizedExperiment, | ||
IRanges, | ||
S4Vectors, | ||
bamsignals, | ||
ComplexHeatmap, | ||
graphics, | ||
stats, | ||
utils | ||
VignetteBuilder: knitr | ||
biocViews: Software, | ||
HistoneModification |