scifer
Bioc currentScifer: Single-Cell Immunoglobulin Filtering of Sanger Sequences
Release Lineage
Entered 3.16 · Nov 2, 2022
Current · Requires R 4.6
Description
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.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
10 7 exported
Complexity
6.6 avg / 21 max
Call network
10 nodes / 4 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
1,818
Files
56
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
7
Internal functions
3
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.36
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
–
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
8
First release
2022-11-01
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
7
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 9includes a package overview page
- Examples that run
- 88%7 run in a plain check · 1 never run
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Repository practices
Checks run against github.com/rodrigarc/scifer on 2026-10-21.
No development-tooling practices detected in the upstream repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| extdata_description | – | – | – |
| test_igblast | data.frame | 13 × 1 | No other package |
Topics
People
- Rodrigo Arcoverde Cerveira author maintainer copyright holder
- Matthew James Hinchcliff contributor
- Karin Loré data contributor thesis advisor funder
- Marcel Martin contributor
- Sebastian Ols author data contributor
Cite
Cite this package
Run in R for the authors' entry:
citation("scifer")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1016/j.immuno.2024.100046.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.