scifer
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see scifer.
Scifer: Single-Cell Immunoglobulin Filtering of Sanger Sequences
Bioconductor version: 3.19
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("scifer")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | FlowCytometry, Preprocessing, QualityControl, SangerSeq, Sequencing, SingleCell, Software |
| Version | 1.6.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (2 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_1.6.0.tar.gz |
| Windows Binary (x86_64) | scifer_1.6.0.zip (64-bit only) |
| macOS Binary (x86_64) | scifer_1.6.0.tgz |
| macOS Binary (arm64) | scifer_1.6.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/scifer |
| Source Repository (Developer Access) | git clone [email protected]:packages/scifer |
| Bioc Package Browser | https://code.bioconductor.org/browse/scifer/ |
| Package Short Url | https://bioconductor.org/packages/scifer/ |
| Package Downloads Report | Download Stats |