scifer

DOI: 10.18129/B9.bioc.scifer    

This is the development version of scifer; for the stable release version, see scifer.

Scifer: Single-Cell Immunoglobulin Filtering of Sanger Sequences

Bioconductor version: Development (3.17)

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.

Author: Rodrigo Arcoverde Cerveira [aut, cre, cph] , Sebastian Ols [aut, dtc] , Karin Loré [dtc, ths]

Maintainer: Rodrigo Arcoverde Cerveira <rodrigo.arcoverdi at gmail.com>

Citation (from within R, enter citation("scifer")):

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("scifer")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF   Reference Manual

Details

biocViews FlowCytometry, Preprocessing, QualityControl, SangerSeq, Sequencing, SingleCell, Software
Version 1.1.0
In Bioconductor since BioC 3.16 (R-4.2) (< 6 months)
License MIT + file LICENSE
Depends
Imports dplyr, rmarkdown, data.table, Biostrings, parallel, stats, plyr, knitr, ggplot2, gridExtra, DECIPHER, stringr, sangerseqR, kableExtra, tibble, scales, rlang, flowCore, methods
LinkingTo
Suggests fs, BiocStyle, testthat (>= 3.0.0)
SystemRequirements
Enhances
URL https://github.com/rodrigarc/scifer
BugReports https://github.com/rodrigarc/scifer/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary
macOS Binary (x86_64) scifer_1.1.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/scifer
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/scifer
Package Short Url https://bioconductor.org/packages/scifer/
Package Downloads Report Download Stats

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