Package: conclus
Title: ScRNA-seq Workflow CONCLUS - From CONsensus CLUSters To A
        Meaningful CONCLUSion
Version: 1.0.0
Authors@R: c(
    person("Ilyess", "Rachedi", email = "ilyessr@hotmail.fr", role = "cre"),
    person("Nicolas", "Descostes", email = "nicolas.descostes@embl.it", role = "aut"),
    person("Polina", " Pavlovich", email = "pavlovich@ie-freiburg.mpg.de", role = "aut"),
    person("Christophe", "Lancrin", email = "christophe.lancrin@embl.it", role = "aut"))
Description: 
    CONCLUS is a tool for robust clustering and positive marker features
    selection of single-cell RNA-seq (sc-RNA-seq) datasets. It takes advantage
    of a consensus clustering approach that greatly simplify sc-RNA-seq data
    analysis for the user. Of note, CONCLUS does not cover the preprocessing
    steps of sequencing files obtained following next-generation sequencing.
    CONCLUS is organized into the following steps:
    Generation of multiple t-SNE plots with a range of parameters including
    different selection of genes extracted from PCA. Use the Density-based
    spatial clustering of applications with noise (DBSCAN) algorithm for
    idenfication of clusters in each generated t-SNE plot. All DBSCAN results
    are combined into a cell similarity matrix. The cell similarity matrix is
    used to define "CONSENSUS" clusters conserved accross the previously
    defined clustering solutions. Identify marker genes for each concensus
    cluster.
Depends: R (>= 4.1)
License: GPL-3
Encoding: UTF-8
RoxygenNote: 7.1.1
Suggests: knitr, rmarkdown, BiocStyle, S4Vectors, matrixStats,
        org.Hs.eg.db, org.Mm.eg.db, dynamicTreeCut, testthat
VignetteBuilder: knitr
Imports: dbscan, fpc, factoextra, Biobase, BiocFileCache, parallel,
        doParallel, foreach, SummarizedExperiment, biomaRt,
        AnnotationDbi, methods, dplyr, scran, scater, pheatmap,
        ggplot2, gridExtra, SingleCellExperiment, stats, utils, scales,
        grDevices, graphics, Rtsne, GEOquery, clusterProfiler, stringr,
        tools
biocViews: Software, Technology, SingleCell, Sequencing, Clustering,
        ATACSeq, Classification
Collate: 'AllClasses.R' 'AllGenerics.R' 'DataFormatting.R'
        'checkFunctions.R' 'constructors.R' 'getters.R' 'globalVar.R'
        'loadDataset.R' 'methods-clustering.R' 'methods-dbscan.R'
        'methods-export.R' 'methods-markers.R'
        'methods-normalization.R' 'sharedInternals.R' 'methods-plot.R'
        'methods-tsne.R' 'runCONCLUS.R' 'setters.R'
git_url: https://git.bioconductor.org/packages/conclus
git_branch: RELEASE_3_13
git_last_commit: 1336595
git_last_commit_date: 2021-05-19
Date/Publication: 2021-05-19
NeedsCompilation: no
Packaged: 2021-05-19 23:14:37 UTC; biocbuild
Author: Ilyess Rachedi [cre],
  Nicolas Descostes [aut],
  Polina Pavlovich [aut],
  Christophe Lancrin [aut]
Maintainer: Ilyess Rachedi <ilyessr@hotmail.fr>
Built: R 4.1.0; ; 2021-05-20 13:41:54 UTC; unix
