Registration Open for Bioc2024 July 24-26


KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline

Bioconductor version: Release (3.19)

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.

Author: Daniel Castillo-Secilla [aut, cre], Juan Manuel Galvez [ctb], Francisco Carrillo-Perez [ctb], Marta Verona-Almeida [ctb], Daniel Redondo-Sanchez [ctb], Francisco Manuel Ortuno [ctb], Luis Javier Herrera [ctb], Ignacio Rojas [ctb]

Maintainer: Daniel Castillo-Secilla <cased at>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

The KnowSeq users guide HTML R Script
Reference Manual PDF


biocViews Alignment, BatchEffect, Classification, DataImport, DifferentialExpression, FeatureExtraction, GO, GeneExpression, GeneSetEnrichment, Genetics, ImmunoOncology, Microarray, Normalization, Pathways, Preprocessing, QualityControl, RNASeq, Sequencing, Software, SystemsBiology, Transcriptomics
Version 1.18.0
In Bioconductor since BioC 3.10 (R-3.6) (4.5 years)
License GPL (>=2)
Depends R (>= 4.0), cqn(>= 1.28.1)
Imports stringr, methods, ggplot2 (>= 3.3.0), jsonlite, kernlab, rlist, rmarkdown, reshape2, e1071, randomForest, caret, XML, praznik, R.utils, httr, sva(>= 3.30.1), edgeR(>= 3.24.3), limma(>= 3.38.3), grDevices, graphics, stats, utils, Hmisc (>= 4.4.0), gridExtra
System Requirements
See More
Suggests knitr
Linking To
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 KnowSeq_1.18.0.tar.gz
Windows Binary
macOS Binary (x86_64) KnowSeq_1.18.0.tgz
macOS Binary (arm64) KnowSeq_1.18.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats