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.
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
1,820
Files
60
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
7
Internal functions
3
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.36
testthat edition
3
CI present
No
CI type
[]
PR gated
No
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
- Examples that run
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- References docs
- 0%
Topics
People
- Rodrigo Arcoverde Cerveira author maintainer cph
- Matthew James Hinchcliff contributor
- Karin Loré dtc ths fnd
- Marcel Martin contributor
- Sebastian Ols author dtc
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("scifer")This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.