DESCRIPTION

Package: transfactor
Title: Transcription factor activity estimator
Version: 0.99.09
Date: 2021-04-21
Authors@R: 
    person(given = "Koen",
           family = "Van den Berge",
           role = c("aut", "cre"),
           email = "koen.vdberge@gmail.com",
           comment = c(ORCID = "0000-0002-1833-8478"))
Description: Estimation of transcription factor (TF) activity by probabilistic assignment of mRNA molecules to the transcription factors that produced them, using a gene regulatory network (GRN). The method allows repressions in the GRN that are incorporated in the TF activity estimation. It also allows the incorporation of prior information on the confidence of each edge in the GRN, to be used in the TF activity estimation.
License: MIT
URL: https://github.com/koenvandenberge/transfactor
BugReports: https://support.bioconductor.org/t/transfactor
biocViews: 
    Software,
    SingleCell,
    Transcriptomics,
    RNASeq
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
Depends:
    SingleCellExperiment,
    glmnet,
    fastmatch,
    arrayhelpers,
    edgeR,
    tibble
Suggests: 
    BiocStyle,
    covr,
    knitr,
    RefManageR,
    rmarkdown,
    sessioninfo,
    testthat (>= 3.0.0),
    MASS
Config/testthat/edition: 3
VignetteBuilder: knitr
Collate: 
    'utils.R'
    'activityEstimationFunctions.R'
    'allGenerics.R'
    'estimateActivity.R'
    'tfCounts.R'
    'tfDistance.R'
    'toyDataForDev.R'
    'utils_revamp.R'