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scifer

Scifer: Single-Cell Immunoglobulin Filtering of Sanger Sequences


Bioconductor version: Release (3.18)

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")

BiocManager::install("scifer")

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("scifer")
Using scifer to filter single-cell sorted B cell receptor (BCR) sanger sequences HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews FlowCytometry, Preprocessing, QualityControl, SangerSeq, Sequencing, SingleCell, Software
Version 1.4.0
In Bioconductor since BioC 3.16 (R-4.2) (1.5 years)
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
System Requirements
URL https://github.com/rodrigarc/scifer
Bug Reports https://github.com/rodrigarc/scifer/issues
See More
Suggests fs, BiocStyle, testthat (>= 3.0.0)
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package scifer_1.4.0.tar.gz
Windows Binary scifer_1.4.0.zip (64-bit only)
macOS Binary (x86_64) scifer_1.4.0.tgz
macOS Binary (arm64) scifer_1.4.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/scifer
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/scifer
Bioc Package Browser https://code.bioconductor.org/browse/scifer/
Package Short Url https://bioconductor.org/packages/scifer/
Package Downloads Report Download Stats