scifer

DOI: 10.18129/B9.bioc.scifer  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see scifer.

Scifer: Single-Cell Immunoglobulin Filtering of Sanger Sequences

Bioconductor version: 3.16

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>

Installation

To install this package, start R (version "4.2") 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")

 

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

Details

biocViews	FlowCytometry, Preprocessing, QualityControl, SangerSeq, Sequencing, SingleCell, Software
Version	1.0.0
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	scifer_1.0.0.tar.gz
Windows Binary	scifer_1.0.0.zip
macOS Binary (x86_64)	scifer_1.0.0.tgz
macOS Binary (arm64)	scifer_1.0.0.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