bioc-issue-bot
commented
9 months ago Hi @xxxmichixxx
Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.
The DESCRIPTION file for this package is:
Package: dinoR
Title: Differential NOMe-seq analysis
Version: 0.99.0
Authors@R:
person("Michaela", "Schwaiger",, "michaela.schwaiger@fmi.ch", role = c("aut", "cre"),
comment = c(ORCID = "0000-0002-4522-7810"))
Description: dinoR tests for significant differences in NOMe-seq
footprints between two conditions,
using genomic regions of interest (ROI) centered around a landmark,
for example a transcription factor (TF) motif.
This package takes NOMe-seq data (GCH methylation/protection) in the form of a Ranged Summarized Experiment as input.
dinoR can be used to group sequencing fragments into 3 or 5 categories representing characteristic footprints (TF bound, nculeosome bound, open chromatin),
plot the percentage of fragments in each category in a heatmap, or averaged across different ROI
groups, for example, containing a common TF motif. It is designed
to compare footprints between two sample groups, using edgeR's quasi-likelihood methods on the total
fragment counts per ROI, sample, and footprint category.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
Suggests:
knitr,
rmarkdown,
testthat (>= 3.0.0)
Config/testthat/edition: 3
VignetteBuilder: knitr
Imports:
BiocGenerics,
circlize,
ComplexHeatmap,
cowplot,
dplyr,
edgeR,
GenomicRanges,
ggplot2,
Matrix,
rlang,
stats,
stringr,
SummarizedExperiment,
tibble,
tidyr,
tidyselect
Depends:
R (>= 4.3.0)
LazyData: false
biocViews:
NucleosomePositioning,
Epigenetics,
MethylSeq,
DifferentialMethylation,
Coverage,
Transcription,
Sequencing,
Software
URL: https://github.com/xxxmichixxx/dinoR
BugReports: https://github.com/xxxmichixxx/dinoR/issues
lshep
xxxmichixxx
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