Package: scifer
Type: Package
Title: Scifer: Single-Cell Immunoglobulin Filtering of Sanger Sequences
Version: 1.12.0
Authors@R: 
    c(person(given = "Rodrigo",
             family = "Arcoverde Cerveira",
             role = c("aut", "cre", "cph"),
             email = "rodrigo.arcoverdi@gmail.com",
             comment = c(ORCID = "0000-0002-1145-2534")),
     person(given = "Marcel",
             family = "Martin",
             role = c("ctb")),
     person(given = "Matthew James",
             family = "Hinchcliff",
             role = c("ctb")),
     person(given = "Sebastian",
             family = "Ols",
             role = c("aut", "dtc"),
             comment = c(ORCID = "0000-0001-9784-7176")),
     person(given = "Karin",
             family = "Loré",
             role = c("dtc", "ths", "fnd"),
             comment = c(ORCID = "0000-0001-7679-9494")))
URL: https://github.com/rodrigarc/scifer
BugReports: https://github.com/rodrigarc/scifer/issues
Description: Have you ever index sorted cells in a 96 or 384-well plate
        and then sequenced using Sanger sequencing? If so, you probably
        had some struggles to either check the electropherogram of each
        cell sequenced manually, or when you tried to identify which
        cell was sorted where after sequencing the plate. Scifer was
        developed to solve this issue by performing basic quality
        control of Sanger sequences and merging flow cytometry data
        from probed single-cell sorted B cells with sequencing data.
        scifer can export summary tables, 'fasta' files,
        electropherograms for visual inspection, and generate reports.
License: MIT + file LICENSE
Encoding: UTF-8
biocViews: Preprocessing, QualityControl, SangerSeq, Sequencing,
        Software, FlowCytometry, SingleCell
Imports: dplyr, rmarkdown, data.table, Biostrings, stats, plyr, knitr,
        ggplot2, gridExtra, DECIPHER, stringr, sangerseqR, kableExtra,
        tibble, scales, rlang, flowCore, methods, basilisk,
        basilisk.utils, reticulate, here, pwalign, utils
RoxygenNote: 7.3.2
VignetteBuilder: knitr
Suggests: BiocBaseUtils, fs, BiocStyle, testthat (>= 3.0.0)
Enhances: parallel
Config/testthat/edition: 3
StagedInstall: no
Config/pak/sysreqs: libfontconfig1-dev libfreetype6-dev libfribidi-dev
        make libharfbuzz-dev libicu-dev libpng-dev libxml2-dev python3
        zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:18:43 UTC
RemoteUrl: https://github.com/bioc/scifer
RemoteRef: RELEASE_3_22
RemoteSha: e09cc12666cc80622f8cff92810b4836cf02afa6
NeedsCompilation: no
Packaged: 2026-01-24 19:59:52 UTC; root
Author: Rodrigo Arcoverde Cerveira [aut, cre, cph] (ORCID:
    <https://orcid.org/0000-0002-1145-2534>),
  Marcel Martin [ctb],
  Matthew James Hinchcliff [ctb],
  Sebastian Ols [aut, dtc] (ORCID:
    <https://orcid.org/0000-0001-9784-7176>),
  Karin Loré [dtc, ths, fnd] (ORCID:
    <https://orcid.org/0000-0001-7679-9494>)
Maintainer: Rodrigo Arcoverde Cerveira <rodrigo.arcoverdi@gmail.com>
Built: R 4.5.2; ; 2026-01-24 20:01:43 UTC; windows
