LedPred: Learning from DNA to Predict Enhancers

This package aims at creating a predictive model of regulatory sequences used to score unknown sequences based on the content of DNA motifs, next-generation sequencing (NGS) peaks and signals and other numerical scores of the sequences using supervised classification. The package contains a workflow based on the support vector machine (SVM) algorithm that maps features to sequences, optimize SVM parameters and feature number and creates a model that can be stored and used to score the regulatory potential of unknown sequences.

AuthorElodie Darbo, Denis Seyres, Aitor Gonzalez
Date of publicationNone
MaintainerAitor Gonzalez <aitor.gonzalez@univ-amu.fr>
LicenseMIT | file LICENSE
Version1.8.0

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Files

LedPred/DESCRIPTION
LedPred/LICENSE
LedPred/NAMESPACE
LedPred/NEWS
LedPred/R
LedPred/R/Data.R LedPred/R/FeatureNbTuner.R LedPred/R/FeatureRanking.R LedPred/R/LedPredClass.R LedPred/R/Model.R LedPred/R/ModelPerformance.R LedPred/R/ParameterTuner.R LedPred/R/createModel.R LedPred/R/evaluateModelPerformance.R LedPred/R/ledpred.R LedPred/R/mapFeaturesToCRMs.R LedPred/R/mcTune.R LedPred/R/rankFeatures.R LedPred/R/scoreData.R LedPred/R/tuneFeatureNb.R
LedPred/build
LedPred/build/vignette.rds
LedPred/data
LedPred/data/crm.features.rda
LedPred/data/feature.ranking.rda
LedPred/inst
LedPred/inst/CITATION
LedPred/inst/doc
LedPred/inst/doc/LedPred.R
LedPred/inst/doc/LedPred.Rnw
LedPred/inst/doc/LedPred.pdf
LedPred/inst/extdata
LedPred/inst/extdata/259_matrices_lightNames.tf
LedPred/inst/extdata/2nt_intergenic_droso.freq
LedPred/inst/extdata/negative_50CADenhancers.bed
LedPred/inst/extdata/ngs
LedPred/inst/extdata/ngs/K4me1_E_F_6_8h_H3_subtracted_reduced.wig
LedPred/inst/extdata/ngs/docBoundCRM.bed
LedPred/inst/extdata/ngs/dtcfBoundCRM.bed
LedPred/inst/extdata/ngs/pmadBoundCRM.bed
LedPred/inst/extdata/ngs/pnrBoundCRM.bed
LedPred/inst/extdata/ngs/tinBoundCRM.bed
LedPred/inst/extdata/positive_50CADenhancers.bed
LedPred/inst/extdata/prediction_small.bed
LedPred/inst/extdata/testdata
LedPred/inst/extdata/testdata/230NonActivesEnhancers4_8h_2seqs.bed
LedPred/inst/extdata/testdata/23From66ActiveEnhancersInMesoAt68h_2seqs.bed
LedPred/inst/extdata/testdata/feature_nb.txt
LedPred/inst/extdata/testdata/feature_rank.txt
LedPred/inst/extdata/testdata/test_ngs_bed_small
LedPred/inst/extdata/testdata/test_ngs_bed_small/mfile2.tf
LedPred/inst/extdata/testdata/test_ngs_bed_small/negative_5seqs.bed
LedPred/inst/extdata/testdata/test_ngs_bed_small/ngs_beds
LedPred/inst/extdata/testdata/test_ngs_bed_small/ngs_beds/ngs.bed
LedPred/inst/extdata/testdata/test_ngs_bed_small/ngs_beds/ngs2.bed
LedPred/inst/extdata/testdata/test_ngs_bed_small/outdir_bak
LedPred/inst/extdata/testdata/test_ngs_bed_small/outdir_bak/feature_matrix.tab
LedPred/inst/extdata/testdata/test_ngs_bed_small/positive_2seqs.bed
LedPred/man
LedPred/man/LedPred.Rd LedPred/man/createModel.Rd LedPred/man/crm.features.Rd LedPred/man/evaluateModelPerformance.Rd LedPred/man/feature.ranking.Rd LedPred/man/mapFeaturesToCRMs.Rd LedPred/man/mcTune.Rd LedPred/man/rankFeatures.Rd LedPred/man/scoreData.Rd LedPred/man/tuneFeatureNb.Rd
LedPred/tests
LedPred/tests/testthat
LedPred/tests/testthat.R
LedPred/tests/testthat/_ROC_perf.png
LedPred/tests/testthat/_kappa_measures.png
LedPred/tests/testthat/data_iris2
LedPred/tests/testthat/data_iris2/feature.ranking.rda
LedPred/tests/testthat/data_iris2/iris2.rda
LedPred/tests/testthat/data_iris2/x.rda
LedPred/tests/testthat/data_iris2/y.rda
LedPred/tests/testthat/test-iris2_Data.R
LedPred/tests/testthat/test-iris2_FeatureNbTuner.R
LedPred/tests/testthat/test-iris2_FeatureRanking.R
LedPred/tests/testthat/test-iris2_LedPred.R
LedPred/tests/testthat/test-iris2_ModelCreate.R
LedPred/tests/testthat/test-iris2_ModelPerformance.R
LedPred/tests/testthat/test-iris2_ParameterTuner.R
LedPred/vignettes
LedPred/vignettes/LedPred.Rnw
LedPred/vignettes/_ROCR_perf.png
LedPred/vignettes/_c_g_eval.png
LedPred/vignettes/_kappa_measures.png
LedPred/vignettes/figs
LedPred/vignettes/figs/vignette_ROC_perf.png
LedPred/vignettes/figs/vignette_c_g_eval.png
LedPred/vignettes/figs/vignette_kappa_measures.png

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.