Files in morphos30/DeepG4
A deep learning approach to predict active G-quadruplexes
.Rbuildignore
.gitignore
DESCRIPTION
DeepG4.Rproj
NAMESPACE
R/DNAToNumerical.R
R/DeepG4.R
R/DeepG4InputFromBED.R
R/DeepG4Scan.R
R/ExtractMotifFromModel.R
R/ExtractSubSequence.R
R/ExtractSubSequencefromBed.R
R/NormBW.R
R/getScoreBW.R
README.Rmd
README.md
best_pcm_from_kernel.svg
codecov.yml
environment.yml
inst/extdata/DeepG4_ATAC_rescale_BW_by_bg_5kb_seuil_2_19_04_2021/2021-04-19T16-32-14Z/best_model.h5
inst/extdata/DeepG4_ATAC_rescale_BW_by_bg_5kb_seuil_2_19_04_2021/2021-04-19T16-32-14Z/logs/train/events.out.tfevents.1618849993.disleg-Precision-Tower-7910.32641.324.v2
inst/extdata/DeepG4_ATAC_rescale_BW_by_bg_5kb_seuil_2_19_04_2021/2021-04-19T16-32-14Z/logs/train/events.out.tfevents.1618850128.disleg-Precision-Tower-7910.32641.24582.v2
inst/extdata/DeepG4_ATAC_rescale_BW_by_bg_5kb_seuil_2_19_04_2021/2021-04-19T16-32-14Z/logs/validation/events.out.tfevents.1618850004.disleg-Precision-Tower-7910.32641.2364.v2
inst/extdata/DeepG4_ATAC_rescale_BW_by_bg_5kb_seuil_2_19_04_2021/2021-04-19T16-32-14Z/plots/Rplot001.png
inst/extdata/DeepG4_ATAC_rescale_BW_by_bg_5kb_seuil_2_19_04_2021/2021-04-19T16-32-14Z/plots/Rplot002.png
inst/extdata/DeepG4_ATAC_rescale_BW_by_bg_5kb_seuil_2_19_04_2021/2021-04-19T16-32-14Z/plots/Rplot003.png
inst/extdata/DeepG4_ATAC_rescale_BW_by_bg_5kb_seuil_2_19_04_2021/2021-04-19T16-32-14Z/plots/Rplot004.png
inst/extdata/DeepG4_ATAC_rescale_BW_by_bg_5kb_seuil_2_19_04_2021/2021-04-19T16-32-14Z/tfruns.d/flags.json
inst/extdata/DeepG4_ATAC_rescale_BW_by_bg_5kb_seuil_2_19_04_2021/2021-04-19T16-32-14Z/tfruns.d/metrics.json
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inst/extdata/DeepG4_ATAC_rescale_BW_by_bg_5kb_seuil_2_19_04_2021/2021-04-19T16-32-14Z/tfruns.d/properties/completed
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inst/extdata/DeepG4_ATAC_rescale_BW_by_bg_5kb_seuil_2_19_04_2021/2021-04-19T16-32-14Z/tfruns.d/properties/end
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inst/extdata/DeepG4_ATAC_rescale_BW_by_bg_5kb_seuil_2_19_04_2021/2021-07-02T08-48-55Z/best_model.h5
inst/extdata/DeepG4_ATAC_rescale_BW_by_bg_5kb_seuil_2_19_04_2021/2021-07-02T08-48-55Z/logs/train/events.out.tfevents.1625215777.disleg-Precision-Tower-7910.9429.324.v2
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inst/extdata/DeepG4_ATAC_rescale_BW_by_bg_5kb_seuil_2_19_04_2021/2021-07-02T08-48-55Z/logs/validation/events.out.tfevents.1625215787.disleg-Precision-Tower-7910.9429.2364.v2
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inst/extdata/DeepG4_ATAC_rescale_BW_by_bg_5kb_seuil_2_19_04_2021/2021-07-02T08-48-55Z/tfruns.d/properties/learning_rate
inst/extdata/DeepG4_ATAC_rescale_BW_by_bg_5kb_seuil_2_19_04_2021/2021-07-02T08-48-55Z/tfruns.d/properties/loss_function
inst/extdata/DeepG4_ATAC_rescale_BW_by_bg_5kb_seuil_2_19_04_2021/2021-07-02T08-48-55Z/tfruns.d/properties/model
inst/extdata/DeepG4_ATAC_rescale_BW_by_bg_5kb_seuil_2_19_04_2021/2021-07-02T08-48-55Z/tfruns.d/properties/optimizer
inst/extdata/DeepG4_ATAC_rescale_BW_by_bg_5kb_seuil_2_19_04_2021/2021-07-02T08-48-55Z/tfruns.d/properties/output
inst/extdata/DeepG4_ATAC_rescale_BW_by_bg_5kb_seuil_2_19_04_2021/2021-07-02T08-48-55Z/tfruns.d/properties/samples
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inst/extdata/DeepG4_ATAC_rescale_BW_by_bg_5kb_seuil_2_19_04_2021/2021-07-06T07-59-11Z/best_model.h5
inst/extdata/DeepG4_ATAC_rescale_BW_by_bg_5kb_seuil_2_19_04_2021/2021-07-06T07-59-11Z/logs/train/events.out.tfevents.1625558354.disleg-Precision-Tower-7910.26324.360324.v2
inst/extdata/DeepG4_ATAC_rescale_BW_by_bg_5kb_seuil_2_19_04_2021/2021-07-06T07-59-11Z/logs/train/events.out.tfevents.1625558551.disleg-Precision-Tower-7910.26324.384480.v2
inst/extdata/DeepG4_ATAC_rescale_BW_by_bg_5kb_seuil_2_19_04_2021/2021-07-06T07-59-11Z/logs/validation/events.out.tfevents.1625558365.disleg-Precision-Tower-7910.26324.362364.v2
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inst/extdata/DeepG4_ATAC_rescale_BW_by_bg_5kb_seuil_2_19_04_2021/2021-07-06T07-59-11Z/plots/Rplot002.png
inst/extdata/DeepG4_ATAC_rescale_BW_by_bg_5kb_seuil_2_19_04_2021/2021-07-06T07-59-11Z/plots/Rplot003.png
inst/extdata/DeepG4_ATAC_rescale_BW_by_bg_5kb_seuil_2_19_04_2021/2021-07-06T07-59-11Z/plots/Rplot004.png
inst/extdata/DeepG4_ATAC_rescale_BW_by_bg_5kb_seuil_2_19_04_2021/2021-07-06T07-59-11Z/tfruns.d/flags.json
inst/extdata/DeepG4_ATAC_rescale_BW_by_bg_5kb_seuil_2_19_04_2021/2021-07-06T07-59-11Z/tfruns.d/metrics.json
inst/extdata/DeepG4_ATAC_rescale_BW_by_bg_5kb_seuil_2_19_04_2021/2021-07-06T07-59-11Z/tfruns.d/properties/batch_size
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inst/extdata/DeepG4_ATAC_rescale_BW_by_bg_5kb_seuil_2_19_04_2021/2021-07-06T07-59-11Z/tfruns.d/properties/epochs
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inst/extdata/DeepG4_ATAC_rescale_BW_sampling_02_03_2021/2021-03-02T16-01-34Z/best_model.h5
inst/extdata/DeepG4_classic_rescale_BW_sampling_02_03_2021/2021-03-02T16-17-28Z/best_model.h5
inst/extdata/Peaks_BG4_G4seq_HaCaT_GSE76688_hg19_201b.bed
inst/extdata/Peaks_BG4_G4seq_HaCaT_GSE76688_hg19_201b_Accessibility.bw
inst/extdata/Peaks_BG4_G4seq_HaCaT_GSE76688_hg19_201b_Ctrl_gkmSVM.bed
inst/extdata/promoters_seq_example.bed
inst/extdata/promoters_seq_example.fa
inst/extdata/random_region_for_scaling_min_max.bed
inst/extdata/test_G4_data.bed
inst/extdata/test_G4_data.fa
logo.svg
man/DNAToNumerical.Rd
man/DeepG4.Rd
man/DeepG4InputFromBED.Rd
man/DeepG4Scan.Rd
man/ExtractMotifFromModel.Rd
man/ExtractSubSequence.Rd
man/ExtractSubSequencefromBed.Rd
man/NormBW.Rd
man/dot-callDeepG4Scan.Rd
man/dot-callDeepG4ScanATAC.Rd
man/getScoreBW.Rd
p_res_train.svg
tests/testthat.R
tests/testthat/test-DNAToNumerical.R
tests/testthat/test-DeepG4.R
tests/testthat/test-DeepG4InputFromBED.R
tests/testthat/test-DeepG4Scan.R
tests/testthat/test-ExtractMotifFromModel.R
tests/testthat/test-NormBW.R
tests/testthat/test-getScoreBW.R
