Package: KnowSeq
Type: Package
Title: KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline
Version: 1.25.0
Authors@R: c(person("Daniel", "Castillo-Secilla", role = c("aut","cre"), 
            email = "cased@ugr.es"), 
        person("Juan Manuel", "Galvez", role="ctb"),
        person("Francisco", "Carrillo-Perez", role="ctb"),
        person("Marta", "Verona-Almeida", role="ctb"),
        person("Daniel", "Redondo-Sanchez", role=c("ctb")),
        person("Francisco Manuel", "Ortuno", role=c("ctb")),
        person("Luis Javier", "Herrera", role=c("ctb")),
        person("Ignacio", "Rojas", role=c("ctb")))
Description: KnowSeq proposes a novel methodology that comprises the
        most relevant steps in the Transcriptomic gene expression
        analysis. KnowSeq expects to serve as an integrative tool that
        allows to process and extract relevant biomarkers, as well as
        to assess them through a Machine Learning approaches. Finally,
        the last objective of KnowSeq is the biological knowledge
        extraction from the biomarkers (Gene Ontology enrichment,
        Pathway listing and Visualization and Evidences related to the
        addressed disease). Although the package allows analyzing all
        the data manually, the main strenght of KnowSeq is the
        possibilty of carrying out an automatic and intelligent HTML
        report that collect all the involved steps in one document. It
        is important to highligh that the pipeline is totally modular
        and flexible, hence it can be started from whichever of the
        different steps. KnowSeq expects to serve as a novel tool to
        help to the experts in the field to acquire robust knowledge
        and conclusions for the data and diseases to study.
License: GPL (>=2)
Depends: R (>= 4.0), cqn (>= 1.28.1)
Encoding: UTF-8
RoxygenNote: 7.1.1
biocViews: GeneExpression, DifferentialExpression, GeneSetEnrichment,
        DataImport, Classification, FeatureExtraction, Sequencing,
        RNASeq, BatchEffect, Normalization, Preprocessing,
        QualityControl, Genetics, Transcriptomics, Microarray,
        Alignment, Pathways, SystemsBiology, GO, ImmunoOncology
Imports: stringr, methods, ggplot2 (>= 3.3.0), jsonlite, kernlab,
        rlist, rmarkdown, reshape2, e1071, randomForest, caret, XML,
        praznik, R.utils, httr, sva (>= 3.30.1), edgeR (>= 3.24.3),
        limma (>= 3.38.3), grDevices, graphics, stats, utils, Hmisc (>=
        4.4.0), gridExtra
VignetteBuilder: knitr
Suggests: knitr
git_url: https://github.com/CasedUgr/KnowSeq
Config/pak/sysreqs: make libicu-dev libpng-dev libxml2-dev libssl-dev
        zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 14:52:51 UTC
RemoteUrl: https://github.com/bioc/KnowSeq
RemoteRef: HEAD
RemoteSha: dda948802ce736875690edcce75b7e851897e95c
NeedsCompilation: no
Packaged: 2026-02-20 08:29:57 UTC; root
Author: Daniel Castillo-Secilla [aut, cre],
  Juan Manuel Galvez [ctb],
  Francisco Carrillo-Perez [ctb],
  Marta Verona-Almeida [ctb],
  Daniel Redondo-Sanchez [ctb],
  Francisco Manuel Ortuno [ctb],
  Luis Javier Herrera [ctb],
  Ignacio Rojas [ctb]
Maintainer: Daniel Castillo-Secilla <cased@ugr.es>
Built: R 4.6.0; ; 2026-02-20 08:32:51 UTC; unix
