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
git_url: https://git.bioconductor.org/packages/scifer
git_branch: RELEASE_3_22
git_last_commit: e09cc12
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.22
Date/Publication: 2025-10-29
NeedsCompilation: no
Packaged: 2025-10-30 05:22:23 UTC; biocbuild
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 4.5.1; ; 2025-10-30 12:38:02 UTC; unix
