first push

.Rbuildignore

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+^LICENSE\.md$
+^README\.Rmd$
+^\.github$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$

.github/.gitignore

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+*.html

.github/CODE_OF_CONDUCT.md

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+The Bioconductor community values
+
+* an open approach to science that promotes the sharing of ideas, code, and expertise
+* collaboration
+* diversity and inclusivity
+* a kind and welcoming environment
+* community contributions
+
+In line with these values, Bioconductor is dedicated to providing a welcoming, supportive, collegial, experience free of harassment, intimidation, and bullying regardless of:
+
+* identity: gender, gender identity and expression, sexual orientation, disability, physical appearance, ethnicity, body size, race, age, religion, etc.
+* intellectual position: approaches to data analysis, software preferences, coding style, scientific perspective, etc.
+* stage of career
+
+In order to uphold these values, members of the Bioconductor community are required to follow the Code of Conduct.The latest version of Bioconductor project Code of Conduct is available at http://bioconductor.org/about/code-of-conduct/. Please read the Code of Conduct before contributing to this project.
+
+Thank you!

.github/workflows/rworkflows.yml

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+name: rworkflows
+'on':
+  push:
+    branches:
+    - master
+    - main
+    - devel
+    - RELEASE_**
+  pull_request:
+    branches:
+    - master
+    - main
+    - devel
+    - RELEASE_**
+jobs:
+  rworkflows:
+    permissions: write-all
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+    container: ${{ matrix.config.cont }}
+    strategy:
+      fail-fast: ${{ false }}
+      matrix:
+        config:
+        - os: ubuntu-latest
+          bioc: devel
+          r: auto
+          cont: ghcr.io/bioconductor/bioconductor_docker:devel
+          rspm: ~
+        - os: macOS-latest
+          bioc: release
+          r: auto
+          cont: ~
+          rspm: ~
+        - os: windows-latest
+          bioc: release
+          r: auto
+          cont: ~
+          rspm: ~
+    steps:
+    - uses: neurogenomics/rworkflows@master
+      with:
+        run_bioccheck: ${{ false }}
+        run_rcmdcheck: ${{ true }}
+        as_cran: ${{ true }}
+        run_vignettes: ${{ true }}
+        has_testthat: ${{ true }}
+        run_covr: ${{ true }}
+        run_pkgdown: ${{ true }}
+        has_runit: ${{ false }}
+        has_latex: ${{ false }}
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run_docker: ${{ false }}
+        DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }}
+        runner_os: ${{ runner.os }}
+        cache_version: cache-v1
+        docker_registry: ghcr.io

.gitignore

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+inst/doc
+docs
+*.pdf
+NOTES.md

DESCRIPTION

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+Package: CoverageExperiment
+Title: Coverage metrics over aligned genomic features of interest 
+Version: 0.98.0
+Date: 2023-11-09
+Authors@R: 
+    person("First", "Last", , "[email protected]", role = c("aut", "cre"),
+           comment = c(ORCID = "YOUR-ORCID-ID"))
+Description: What the package does (one paragraph).
+License: MIT + file LICENSE
+URL: 
+BugReports: https://support.bioconductor.org/tag/CoverageExperiment
+biocViews: Software
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.2.3
+Depends: 
+    R (>= 2.10),
+    SummarizedExperiment
+Imports: 
+    S4Vectors, 
+    IRanges,
+    GenomicRanges,
+    GenomeInfoDb, 
+    BiocParallel, 
+    methods,
+    dplyr,
+    fansi, 
+    pillar, 
+    rlang, 
+    cli, 
+    purrr, 
+    vctrs
+Suggests: 
+    tidySummarizedExperiment,
+    plyranges,
+    rtracklayer,
+    ggplot2,
+    TxDb.Hsapiens.UCSC.hg19.knownGene,
+    AnnotationHub,
+    GenomicFeatures, 
+    BiocStyle,
+    knitr,
+    rmarkdown,
+    sessioninfo,
+    testthat (>= 3.0.0)
+Config/testthat/edition: 3
+VignetteBuilder: knitr
+LazyData: false
+Collate: 
+    'AllClasses.R'
+    'AllGenerics.R'
+    'AllMethods.R'
+    'CoverageExperiment.R'
+    'aggregate.R'
+    'data.R'
+    'globals.R'
+    'print.R'
+    'reexports.R'
+    'utils.R'

LICENSE

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+YEAR: 2023
+COPYRIGHT HOLDER: CoverageExperiment authors

LICENSE.md

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+# MIT License
+
+Copyright (c) 2023 CoverageExperiment authors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+S3method(as_tibble,CoverageExperiment)
+S3method(print,CoverageExperiment)
+S3method(tbl_format_header,tidyCoverageExperiment)
+export(CoverageExperiment)
+export(aggregate)
+export(as_tibble)
+exportMethods(CoverageExperiment)
+exportMethods(aggregate)
+exportMethods(show)
+import(GenomeInfoDb)
+import(GenomicRanges)
+import(SummarizedExperiment)
+import(methods)
+importFrom(BiocParallel,bplapply)
+importFrom(BiocParallel,bpparam)
+importFrom(IRanges,NumericList)
+importFrom(S4Vectors,aggregate)
+importFrom(SummarizedExperiment,assayNames)
+importFrom(cli,console_width)
+importFrom(cli,symbol)
+importFrom(dplyr,as_tibble)
+importFrom(dplyr,bind_cols)
+importFrom(dplyr,bind_rows)
+importFrom(dplyr,filter)
+importFrom(dplyr,mutate)
+importFrom(dplyr,relocate)
+importFrom(fansi,strwrap_ctl)
+importFrom(pillar,align)
+importFrom(pillar,get_extent)
+importFrom(pillar,style_subtle)
+importFrom(pillar,tbl_format_header)
+importFrom(purrr,map_chr)
+importFrom(rlang,names2)
+importFrom(stats,qt)
+importFrom(stats,setNames)
+importFrom(vctrs,new_data_frame)

R/AllClasses.R

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+methods::setClass(
+    "CoverageExperiment", 
+    contains = c("RangedSummarizedExperiment")
+)

R/AllGenerics.R

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+#' @export 
+setGeneric("CoverageExperiment", function(tracks, features, ...) standardGeneric("CoverageExperiment"))

R/AllMethods.R

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+#' as_tibble
+#' 
+#' Coerce an `CoverageExperiment` object into a `tibble`
+#' 
+#' @rdname as_tibble
+#' 
+#' @param x an `CoverageExperiment` object
+#' @param ... ignored
+#' @return `tibble`
+#' 
+#' @importFrom dplyr as_tibble
+#' @export
+#' @examples 
+#' data(ac)
+#' as_tibble(ac)
+
+as_tibble.CoverageExperiment <- function(x, ...) {
+    tracks <- colData(x)$track
+    features <- rowData(x)$features
+    assays <- names(assays(x))
+    w <- width(rowRanges(x)[[1]])[[1]]
+    bin <- w / length(assay(x, 1)[1, 1][[1]])
+    lapply(tracks, function(t) {
+        lapply(features, function(f) {
+            lapply(assays(x), `[[`, f, t) |> 
+                stats::setNames(assays) |> 
+                dplyr::bind_cols() |> 
+                dplyr::mutate(
+                    coord = seq(-w/2, w/2-1, bin), 
+                    track = t, features = f
+                ) |> 
+                dplyr::relocate(coord) |> 
+                dplyr::relocate(features) |> 
+                dplyr::relocate(track)
+        }) |> dplyr::bind_rows()
+    }) |> dplyr::bind_rows()
+}
+
+#' show
+#' 
+#' show method for `CoverageExperiment` objects
+#' 
+#' @rdname show
+#' 
+#' @param object a CoverageExperiment object
+#' @return `tibble`
+#' 
+#' @export
+
+setMethod("show", signature("CoverageExperiment"), function(object) {
+    w <- width(rowRanges(object)[[1]][1])
+    b <- w / ncol(assay(object, "coverage")[1, 1][[1]])
+    if (
+        isTRUE(x = getOption(x = "restore_SummarizedExperiment_show", default = FALSE)) | 
+        isTRUE(x = getOption(x = "restore_CoverageExperiment_show", default = FALSE)) | 
+        isFALSE("tidySummarizedExperiment" %in% .packages())
+    ) {
+        f <- getMethod(f = "show", signature = "SummarizedExperiment", 
+            where = asNamespace(ns = "SummarizedExperiment"))
+        f(object = object)
+        cat(paste0("width: ", w, '\n'))
+        cat(paste0("binning: ", b, '\n'))
+    }
+    else {
+        print(object)
+    }
+})