Package: BgeeCall Type: Package Title: Automatic RNA-Seq present/absent gene expression calls generation Version: 1.29.3 Date: 2021-05 Authors@R: c(person("Julien", "Wollbrett", role = c("aut", "cre"), email = "julien.wollbrett@unil.ch"), person("Alessandro", "Brandulas Cammarata", role = "aut", email = "alessandro.brandulascammarata@unil.ch"), person("Sara", "Fonseca Costa", role = "aut"), person("Julien", "Roux", role = "aut"), person("Marc", "Robinson Rechavi", role = "ctb"), person("Frederic", "Bastian", role = "aut")) Description: BgeeCall allows to generate present/absent gene expression calls without using an arbitrary cutoff like TPM<1. Calls are generated based on reference intergenic sequences. These sequences are generated based on expression of all RNA-Seq libraries of each species integrated in Bgee (https://bgee.org). Depends: R (>= 3.6) Imports: AnnotationDbi, curl, ggplot2, scales, GenomicFeatures, tximport, Biostrings, readr, sjmisc, RCurl, RSQLite, tools, stringr, rtracklayer, jsonlite, methods, dplyr, data.table, sjmisc, grDevices, graphics, stats, utils, rslurm, rhdf5, txdbmaker, IRanges, spatstat.univar License: GPL-3 + file LICENSE URL: https://github.com/BgeeDB/BgeeCall BugReports: https://github.com/BgeeDB/BgeeCall/issues VignetteBuilder: knitr biocViews: Software, GeneExpression, RNASeq Suggests: knitr, testthat, rmarkdown, AnnotationHub, GenomeInfoDb, httr Encoding: UTF-8 NeedsCompilation: no SystemRequirements: kallisto Roxygen: list(roclets = c("namespace", "rd")) Config/roxygen2/version: 8.0.0 Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libpng-dev libxml2-dev libssl-dev libx11-dev xz-utils zlib1g-dev Repository: https://bioc.r-universe.dev Date/Publication: 2026-07-03 08:24:50 UTC RemoteUrl: https://github.com/bioc/BgeeCall RemoteRef: HEAD RemoteSha: e8d01ba739f7cd677f59e6691471f4242f4b9c07 Packaged: 2026-07-03 12:14:21 UTC; root Author: Julien Wollbrett [aut, cre], Alessandro Brandulas Cammarata [aut], Sara Fonseca Costa [aut], Julien Roux [aut], Marc Robinson Rechavi [ctb], Frederic Bastian [aut] Maintainer: Julien Wollbrett