Package: GRaNIE
Title: GRaNIE: Reconstruction cell type specific gene regulatory
        networks including enhancers using single-cell or bulk
        chromatin accessibility and RNA-seq data
Version: 1.14.0
Encoding: UTF-8
Authors@R: c(person("Christian", "Arnold", email =
        "chrarnold@web.de", role = c("cre","aut")),
        person("Judith", "Zaugg", email =
        "judith.zaugg@embl.de", role = c("aut")),
        person("Rim", "Moussa", email =
        "rim.moussa01@gmail.com", role = "aut"),
        person("Armando", "Reyes-Palomares", email =
        "armandorp@gmail.com", role = "ctb"),
        person("Giovanni", "Palla", email =
        "giov.pll@gmail.com", role = "ctb"),
        person("Maksim", "Kholmatov", email =
        "maksim.kholmatov@embl.de", role = "ctb"))
Description: Genetic variants associated with diseases often affect
        non-coding regions, thus likely having a regulatory role. To
        understand the effects of genetic variants in these regulatory
        regions, identifying genes that are modulated by specific
        regulatory elements (REs) is crucial. The effect of gene
        regulatory elements, such as enhancers, is often cell-type
        specific, likely because the combinations of transcription
        factors (TFs) that are regulating a given enhancer have
        cell-type specific activity. This TF activity can be quantified
        with existing tools such as diffTF and captures differences in
        binding of a TF in open chromatin regions. Collectively, this
        forms a gene regulatory network (GRN) with cell-type and
        data-specific TF-RE and RE-gene links. Here, we reconstruct
        such a GRN using single-cell or bulk RNAseq and open chromatin
        (e.g., using ATACseq or ChIPseq for open chromatin marks) and
        optionally (Capture) Hi-C data. Our network contains different
        types of links, connecting TFs to regulatory elements, the
        latter of which is connected to genes in the vicinity or within
        the same chromatin domain (TAD). We use a statistical framework
        to assign empirical FDRs and weights to all links using a
        permutation-based approach.
Imports: futile.logger, checkmate, patchwork (>= 1.2.0), reshape2,
        data.table, matrixStats, Matrix, GenomicRanges, RColorBrewer,
        ComplexHeatmap, DESeq2, circlize, progress, utils, methods,
        stringr, tools, scales, igraph, S4Vectors, ggplot2, rlang,
        Biostrings, GenomeInfoDb (>= 1.34.8), SummarizedExperiment,
        forcats, gridExtra, limma, tidyselect, readr, grid, tidyr (>=
        1.3.0), dplyr, stats, grDevices, graphics, magrittr, tibble,
        viridis, colorspace, biomaRt, topGO, AnnotationHub, ensembldb
Depends: R (>= 4.2.0)
Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19,
        BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm39,
        BSgenome.Mmusculus.UCSC.mm10, BSgenome.Mmusculus.UCSC.mm9,
        BSgenome.Rnorvegicus.UCSC.rn6, BSgenome.Rnorvegicus.UCSC.rn7,
        BSgenome.Dmelanogaster.UCSC.dm6,
        BSgenome.Mmulatta.UCSC.rheMac10,
        TxDb.Hsapiens.UCSC.hg19.knownGene,
        TxDb.Hsapiens.UCSC.hg38.knownGene,
        TxDb.Mmusculus.UCSC.mm39.knownGene,
        TxDb.Mmusculus.UCSC.mm10.knownGene,
        TxDb.Mmusculus.UCSC.mm9.knownGene,
        TxDb.Rnorvegicus.UCSC.rn6.refGene,
        TxDb.Rnorvegicus.UCSC.rn7.refGene,
        TxDb.Dmelanogaster.UCSC.dm6.ensGene,
        TxDb.Mmulatta.UCSC.rheMac10.refGene, org.Hs.eg.db,
        org.Mm.eg.db, org.Rn.eg.db, org.Dm.eg.db, org.Mmu.eg.db, IHW,
        clusterProfiler, ReactomePA, DOSE, BiocFileCache, ChIPseeker,
        testthat (>= 3.0.0), BiocStyle, csaw, BiocParallel, WGCNA,
        variancePartition, purrr, EDASeq, JASPAR2022, JASPAR2024,
        RSQLite, TFBSTools, motifmatchr, rbioapi, LDlinkR
VignetteBuilder: knitr
biocViews: Software, GeneExpression, GeneRegulation, NetworkInference,
        GeneSetEnrichment, BiomedicalInformatics, Genetics,
        Transcriptomics, ATACSeq, RNASeq, GraphAndNetwork, Regression,
        Transcription, ChIPSeq
License: Artistic-2.0
URL: https://grp-zaugg.embl-community.io/GRaNIE
BugReports: https://git.embl.de/grp-zaugg/GRaNIE/issues
RoxygenNote: 7.3.1
Config/testthat/parallel: true
Config/testthat/edition: 3
Config/pak/sysreqs: libglpk-dev make libbz2-dev libicu-dev liblzma-dev
        libpng-dev libxml2-dev libssl-dev perl libx11-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:16:56 UTC
RemoteUrl: https://github.com/bioc/GRaNIE
RemoteRef: RELEASE_3_22
RemoteSha: 7d55accfbdf9aa0c5b057a80dba2d55533b86418
NeedsCompilation: no
Packaged: 2025-11-11 20:35:19 UTC; root
Author: Christian Arnold [cre, aut],
  Judith Zaugg [aut],
  Rim Moussa [aut],
  Armando Reyes-Palomares [ctb],
  Giovanni Palla [ctb],
  Maksim Kholmatov [ctb]
Maintainer: Christian Arnold <chrarnold@web.de>
Built: R 4.5.2; ; 2025-11-12 03:37:15 UTC; windows
