scifer

This is the released version of scifer; for the devel version, see scifer.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16

Scifer: Single-Cell Immunoglobulin Filtering of Sanger Sequences

Bioconductor version: Release (3.23)

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] ORCID: 0000-0002-1145-2534 , Marcel Martin [ctb], Matthew James Hinchcliff [ctb], Sebastian Ols [aut, dtc] ORCID: 0000-0001-9784-7176 , Karin Loré [dtc, ths, fnd] ORCID: 0000-0001-7679-9494

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

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

Rodrigo Arcoverde Cerveira, Sebastian Ols. scifer: Scifer: Single-Cell Immunoglobulin Filtering of Sanger Sequences. doi:10.18129/B9.bioc.scifer, R package version 1.14.0, https://bioconductor.org/packages/scifer.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	FlowCytometry, Preprocessing, QualityControl, SangerSeq, Sequencing, SingleCell, Software
Version	1.14.0
In Bioconductor since	BioC 3.16 (R-4.2) (4 years)
License	MIT + file LICENSE
Depends
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
System Requirements
URL	https://github.com/rodrigarc/scifer
Bug Reports	https://github.com/rodrigarc/scifer/issues

Suggests	BiocBaseUtils, fs, BiocStyle, testthat (>= 3.0.0)
Linking To
Enhances	parallel
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	scifer_1.14.0.tar.gz
Windows Binary (x86_64)	scifer_1.14.0.zip
macOS Binary (big-sur-x86_64)	scifer_1.14.0.tgz
macOS Binary (sonoma-arm64)	scifer_1.14.0.tgz
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