KnowSeq

DOI: 10.18129/B9.bioc.KnowSeq    

This is the development version of KnowSeq; for the stable release version, see KnowSeq.

KnowSeq R/Bioc package: Beyond the traditional Transcriptomic pipeline

Bioconductor version: Development (3.12)

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, Juan Manuel Galvez, Francisco Carrillo-Perez, Marta Verona-Almeida, Francisco Manuel Ortuno, Luis Javier Herrera and Ignacio Rojas.

Maintainer: Daniel Castillo-Secilla <cased at ugr.es>

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

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("KnowSeq")

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("KnowSeq")

 

HTML R Script The KnowSeq users guide
PDF   Reference Manual
Text   NEWS

Details

biocViews Alignment, BatchEffect, Classification, DataImport, DifferentialExpression, FeatureExtraction, GO, GeneExpression, GeneSetEnrichment, Genetics, ImmunoOncology, Microarray, Normalization, Pathways, Preprocessing, QualityControl, RNASeq, Sequencing, Software, SystemsBiology, Transcriptomics
Version 1.3.1
In Bioconductor since BioC 3.10 (R-3.6) (1 year)
License GPL (>=2)
Depends R (>= 4.0), cqn(>= 1.28.1)
Imports stringr, kernlab, ggplot2 (>= 3.3.0), rlist, rmarkdown, reshape2, gplots, caret, RCurl, XML, class, praznik, R.utils, e1071, randomForest, httr, jsonlite, sva(>= 3.30.1), edgeR(>= 3.24.3), limma(>= 3.38.3), Biobase, multtest, pathview(>= 1.22.3), grDevices, graphics, stats, utils, Hmisc (>= 4.4.0), gridExtra
LinkingTo
Suggests knitr
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package KnowSeq_1.3.1.tar.gz
Windows Binary KnowSeq_1.3.1.zip
macOS 10.13 (High Sierra) KnowSeq_1.3.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/KnowSeq
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/KnowSeq
Package Short Url https://bioconductor.org/packages/KnowSeq/
Package Downloads Report Download Stats

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