KnowSeq
Bioc currentKnowSeq R/Bioc package: The Smart Transcriptomic Pipeline
Release Lineage
Entered 3.10 · Oct 30, 2019
Current · Requires R 4.6
Description
KnowSeq proposes a novel methodology that comprises the most relevant steps in the Transcriptomic gene expression analysis. KnowSeq expects to serve as an integrative tool that allows to process and extract relevant biomarkers, as well as to assess them through a Machine Learning approaches. Finally, the last objective of KnowSeq is the biological knowledge extraction from the biomarkers (Gene Ontology enrichment, Pathway listing and Visualization and Evidences related to the addressed disease). Although the package allows analyzing all the data manually, the main strenght of KnowSeq is the possibilty of carrying out an automatic and intelligent HTML report that collect all the involved steps in one document. It is important to highligh that the pipeline is totally modular and flexible, hence it can be started from whichever of the different steps. KnowSeq expects to serve as a novel tool to help to the experts in the field to acquire robust knowledge and conclusions for the data and diseases to study.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
26 26 exported
Complexity
23.5 avg / 114 max
Call network
26 nodes / 24 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
6,307
Files
83
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
26
Internal functions
0
Testing & CI
Has tests
No
Test-to-code ratio
0.00
testthat edition
–
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
24
Dep constraint coverage
24%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.0
System requirements
–
C++ standard
–
License
GPL (>=2)
License flags
not SPDX, not OSI
History
Versions
14
First release
2020-02-13
Latest release
2026-04-28
Avg cadence
181 days
Cold removal rate
100%
Dep drift
22
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Examples that run
- 92%
- Documented parameters
- 99%
- Return-value docs
- 100%
- References docs
- 0%
Topics
People
- Daniel Castillo-Secilla author maintainer
- Francisco Carrillo-Perez contributor
- Juan Manuel Galvez contributor
- Luis Javier Herrera contributor
- Francisco Manuel Ortuno contributor
- Daniel Redondo-Sanchez contributor
- Ignacio Rojas contributor
- Marta Verona-Almeida contributor
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("KnowSeq")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.