Package: ECLIPSE
Title: ECLIPSE: Enhanced CLonotypic Inference via Prediction of
        Single-cell Expression
Version: 0.99.0
Authors@R: c(
    person("Ethan", "Burns", comment = c(ORCID = "0009-0009-8061-3686"), email = "ethan.burns@yale.edu", role = c("aut", "cre")),
    person("Zhaochen", "Ye", comment = c(ORCID = "0009-0000-4422-3861"), email = "zhaochen.ye@yale.edu", role = "ctb"),
    person("Kelly", "Street", comment = c(ORCID = "0000-0001-6379-5013"), email = "kelly.street@gmail.com", role = "ctb"),
    person("David", "Braun", comment = c(ORCID = "0000-0003-4543-5553"), email = "david.braun@yale.edu", role = c("aut", "fnd")))
Description: This package is used for the analysis of single-cell T
        cell receptor sequencing data (scTCR-seq). ECLIPSE maps chain
        pairings across a sample to predict the true clonotype of each
        cell, unlike other methods which only consider the chains that
        are sequenced in each cell. Seurat objects and Cell Ranger
        vdj/multi contig files are required as inputs.
License: GPL (>= 3)
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
Imports: dplyr, ggplot2, scRepertoire, stringr, tidyr, VDJdive,
        methods, rlang, testthat, BiocStyle, tidyselect, magrittr
URL: https://github.com/eburns10/ECLIPSE
biocViews: Software, GeneExpression, BiomedicalInformatics,
        ImmunoOncology, Transcriptomics, Classification, SingleCell,
        Annotation, Sequencing
BugReports: https://github.com/eburns10/ECLIPSE/issues
Depends: R (>= 4.4.0)
Config/roxygen2/version: 8.0.0
Suggests: knitr, rmarkdown, ragg, tidyverse, remotes
VignetteBuilder: knitr
RoxygenNote: 8.0.0
Config/pak/sysreqs: cmake libfontconfig1-dev libfreetype6-dev
        libglpk-dev make libgsl0-dev libicu-dev libuv1-dev libxml2-dev
        libssl-dev zlib1g-dev
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-08-11 16:21:03 UTC
RemoteUrl: https://github.com/BiocStaging/ECLIPSE
RemoteRef: HEAD
RemoteSha: 7f479a65a103929141e892a777f36cd546141857
NeedsCompilation: no
Packaged: 2026-10-11 15:58:53 UTC; root
Author: Ethan Burns [aut, cre] (ORCID: <https://orcid.org/0009-0009-8061-3686>),
  Zhaochen Ye [ctb] (ORCID: <https://orcid.org/0009-0000-4422-3861>),
  Kelly Street [ctb] (ORCID: <https://orcid.org/0000-0001-6379-5013>),
  David Braun [aut, fnd] (ORCID: <https://orcid.org/0000-0003-4543-5553>)
Maintainer: Ethan Burns <ethan.burns@yale.edu>