Institute of Bioinformatics

KeBABS - An R Package for Kernel-Based Analysis of Biological Sequences

The kebabs package provides functionality for kernel based analysis of biological sequences via Support Vector Machine (SVM) based methods. Biological sequences include DNA, RNA, and amino acid (AA) sequences. Sequence kernels define similarity measures between sequences. The package implements some of the most important kernels for sequence analysis in a very flexible and efficient way and extends the standard position-independent functionality of these kernels in a novel way to take the position of patterns in the sequences into account for the similarity measure.

Installation

The R package kebabs is available from Bioconductor. The first version of the package has been released as part of Bioconductor 3.0 on October 14, 2014. The current release version is 1.12.0 (released on October 31, 2017, as part of Bioconductor 3.6). To install kebabs, follow the simple standard procedure for installing Bioconductor packages, i.e. enter the following into your R session:

source("http://www.bioconductor.org/biocLite.R")
biocLite("kebabs")

Please note that Bioconductor 3.6 requires R version 3.4.2.

The current development version of the package is 1.13.0.

Documentation

User Manual: PDF
Reference Manual: PDF

Getting started

To load the package, enter "library(kebabs)" in your R session.
To view the user manual, enter "vignette("kebabs")".
To do a first example, enter "example(kebabs)".

User support

If you encounter any issues or if you have any question that might be of interest also for other users, before writing a private message to the package developers/maintainers, please consider posting on Bioconductor Support or StackOverflow. For all other matters regarding the package, please contact [email protected].

Citing this package

If you use this package for research that is published later, you are kindly asked to cite it as follows:

J. Palme, S. Hochreiter, and U. Bodenhofer (2015). KeBABS: an R package for kernel-based analysis of biological sequences. Bioinformatics 31(15):2574-2576. DOI: 10.1093/bioinformatics/btv176.

R source code for example on epitope-to-MHC binding: A0201-Example.zip (3.7 KB; see file README.txt for more information)

Change log

Version 1.12.0:

release as part of Bioconductor 3.6

Version 1.11.0:

devel branch created from version 1.10.0

Version 1.10.0:

release as part of Bioconductor 3.5

Version 1.9.0:

devel branch created from version 1.8.0

Version 1.8.0:

release as part of Bioconductor 3.4

Version 1.7.0:

devel branch created from version 1.6.2

Version 1.6.1 / 1.6.2:

version number bumps for technical reasons related to Bioconductor build servers

Version 1.6.0:

release as part of Bioconductor 3.3

Version 1.5.4:

importing apcluster package for avoiding method clashes
improved and completed change history in inst/NEWS and package vignette

Version 1.5.3:

correction in prediction via feature weights for very large sparse explicit representation
adaption of vignette template
vignette engine changed from Sweave to knitr

Version 1.5.2:

correction in distance weights for mixed distance weighted spectrum and gappy pair kernel
allow featureWeights as numeric vector for method getPredictionProfile
correction for plot of single prediction profile without legend
change of copyright note
namespace fixes

Version 1.5.1:

new method to compute prediction profiles from models trained with mixture kernels
correction for position specific kernel with offsets
corrections for prediction profile of motif kernel
additional hint on help page of kbsvm

Version 1.5.0:

devel branch created from version 1.4.0

Version 1.4.0:

release as part of Bioconductor 3.2

Version 1.3.4:

correction of Ubuntu problem with realloc for 0 elements in linearKernel generating a sparse empty kernel matrix
correction of problem with feature weights and prediction profiles for position specific gappy pair kernel
orrection of problem with feature weights and prediction profiles for position specific motif kernel
corrections for feature weights, prediction via feature weights and prediction profile for distance weighted kernels
update of KeBABS citation

Version 1.3.3:

new export kebabsCollectInfo for collection of package info
update of version dependency to Biostrings, XVector, S4Vector
correction for leading + or - in factor label
change of bibtex style sheet in vignette to plainnat.bst

Version 1.3.2:

correction of error in kernel lists
user defined sequence kernel example SpectrumKernlabKernel moved to separate directory

Version 1.3.1:

correction of error in model selection for processing via dense LIBSVM
remove problem in check for loading of SparseM

Version 1.3.0:

devel branch created from version 1.2.0

Version 1.2.0:

release as part of Bioconductor 3.1

Version 1.1.9:

inclusion of dense LIBSVM 3.20 for dense kernel matrix support to provide a reliable way for training with kernel matrices
new accessors folds and performance for CrossValidationResult
removed fold performance from show of CV result
adaptions for user defined sequence kernel with new export isUserDefined, example in inst/examples/UserDefinedKernel
correction of errors with position offset for position specific kernels
computation of AUC via trapezoidal rule
changes for auto mode in CV, grid search, model selection
check for non-negative mixing coefficients in spectrum and gappy pair kernel
build warnings on Windows removed
added definition of performance parameters for binary and multiclass classification to vignette
update of citation file and reference section in help pages

Version 1.1.8:

new accessors selGridRow, selGridCol and fullModel for class ModelSelectionResult
change of naming of feature weights because of change in LiblineaR 1.94-2
GCC warnings in Linux removed

Version 1.1.7:

change in LiblineaR - upgrade to LIBLINEAR 1.94 in function LiblineaR the parameter labels was renamed to target
correction in model selection for performance parameters
error correction of vector length overflow in sparse explicit representation for very large number of sequences in spectrum, gappy pair and motif kernel
error correction for AUC in cross validation
minor changes in help pages
minor changes in vignette

Version 1.1.6:

error correction for training with position specific kernel and computation of feature weights
error correction in coercion of kernel to character for distance weighting
error correction in spectrum, gappy pair and motif kernel for kernel matrix - last feature was missing in kernel value in rare situations
correction of Windows build problem in linearKernel
build warnings on Windows removed
minor changes in help pages
minor changes in vignette

Version 1.1.5

new method heatmap to display heatmap of prediction profiles
extension of function linearKernel to optionally return a sparse kernel matrix
correction of computation of feature weights for LiblineaR with more than 3 classes
new accessor SVindex for class KBModel
correction in subsetting of sparse explicit representation for head / tail
error correction in subsetting of prediction profile
error correction in mismatch kernel
heck uniqueness of motifs in motif kernel
minor changes in help pages
change name of vignette Rnw to lowercase
minor changes in vignette

Version 1.1.4:

added two help pages

Version 1.1.3:

fix to adapt for changed Biostrings/S4Vectors API

Version 1.1.2:

minor C code changes for mismatch kernel
correction of MCC
new class ROCData and new function computeROCandAUC for binary classification added
new plot function for ROCData to plot ROC for binary classes
AUC as additional performance parameter in cross validation and as performance objective in grid search

Version 1.1.1:

correction for cross validation with factor label
correction for storing prob model in kebabs model for kernlab
removal of clang warnings for unused functions

Version 1.1.0:

devel branch created from version 1.0.00

Version 1.0.0:

first official release as part of Bioconductor 3.0