├── README.md ├── articles ├── BiRen.pdf ├── DanQ.pdf ├── DeFine.pdf ├── DeepBind.pdf ├── DeepBind_supp.pdf ├── DeepCpG.pdf ├── DeepSEA.pdf ├── DeepTACT.pdf ├── MRCNN.pdf ├── RNA-Seq_review.pdf ├── article_DeepG4.pdf ├── chipseq_review.pdf ├── dilated_conv.pdf ├── eval_deeplearning.pdf ├── intro_deeplearning.pdf └── whataremotifs.pdf ├── data ├── SNP │ ├── ASB.auto.v2.1.aug16.txt.tgz │ ├── GSE31388_dsQtlTableLong.txt.gz │ └── gwas_catalog_v1.0-associations_e100_r2021-01-29.tsv.gz ├── bed │ ├── CTCF_GM12878_hg19_4000_neg.bed │ ├── CTCF_GM12878_hg19_4000_pos.bed │ ├── DNase_GM12878_hg19_4000_neg.bed │ ├── DNase_GM12878_hg19_4000_pos.bed │ ├── DSBCapture_NHEK_hg19_4000_neg.bed │ ├── DSBCapture_NHEK_hg19_4000_pos.bed │ ├── H3K4me3_GM12878_hg19_4000_neg.bed │ ├── H3K4me3_GM12878_hg19_4000_pos.bed │ ├── POL2_GM12878_hg19_4000_neg.bed │ └── POL2_GM12878_hg19_4000_pos.bed ├── fasta │ ├── CTCF_GM12878_hg19_4000_neg.fa │ ├── CTCF_GM12878_hg19_4000_pos.fa │ ├── DNase_GM12878_hg19_4000_neg.fa │ ├── DNase_GM12878_hg19_4000_pos.fa │ ├── DSBCapture_NHEK_hg19_4000_neg.fa │ ├── DSBCapture_NHEK_hg19_4000_pos.fa │ ├── H3K4me3_GM12878_hg19_4000_neg.fa │ ├── H3K4me3_GM12878_hg19_4000_pos.fa │ ├── POL2_GM12878_hg19_4000_neg.fa │ ├── POL2_GM12878_hg19_4000_pos.fa │ ├── sequences_SNPalt_hg19.fa │ └── sequences_SNPref_hg19.fa └── narrowPeak │ ├── CTCF_GM12878_hg19.narrowPeak │ ├── DNase_GM12878_hg19.narrowPeak │ ├── DSBCapture_NHEK_hg19.narrowPeak │ ├── H3K4me3_GM12878_hg19.narrowPeak │ ├── JUND_GM12878_hg19.narrowPeak │ ├── P300_GM12878_hg19.narrowPeak │ └── POL2_GM12878_hg19.narrowPeak ├── header_googlesites.png └── results ├── SNP ├── mutationMap_201b_DNase.pdf └── mutationMap_41b_DNase.pdf ├── model ├── CNN1_model_CTCF.hdf5 ├── CNN1_model_DNase.hdf5 ├── CNN1_model_H3K4me3.hdf5 └── CNN1_model_POL2.hdf5 └── motif ├── root_motifs_DNase.tf ├── trimmed_redundant_motifs_CTCF.tf ├── trimmed_redundant_motifs_DNase.tf ├── trimmed_redundant_motifs_H3K4me3.tf └── trimmed_redundant_motifs_POL2.tf /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/README.md -------------------------------------------------------------------------------- /articles/BiRen.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/articles/BiRen.pdf -------------------------------------------------------------------------------- /articles/DanQ.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/articles/DanQ.pdf -------------------------------------------------------------------------------- /articles/DeFine.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/articles/DeFine.pdf -------------------------------------------------------------------------------- /articles/DeepBind.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/articles/DeepBind.pdf -------------------------------------------------------------------------------- /articles/DeepBind_supp.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/articles/DeepBind_supp.pdf -------------------------------------------------------------------------------- /articles/DeepCpG.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/articles/DeepCpG.pdf -------------------------------------------------------------------------------- /articles/DeepSEA.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/articles/DeepSEA.pdf -------------------------------------------------------------------------------- /articles/DeepTACT.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/articles/DeepTACT.pdf -------------------------------------------------------------------------------- /articles/MRCNN.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/articles/MRCNN.pdf -------------------------------------------------------------------------------- /articles/RNA-Seq_review.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/articles/RNA-Seq_review.pdf -------------------------------------------------------------------------------- /articles/article_DeepG4.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/articles/article_DeepG4.pdf -------------------------------------------------------------------------------- /articles/chipseq_review.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/articles/chipseq_review.pdf -------------------------------------------------------------------------------- /articles/dilated_conv.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/articles/dilated_conv.pdf -------------------------------------------------------------------------------- /articles/eval_deeplearning.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/articles/eval_deeplearning.pdf -------------------------------------------------------------------------------- /articles/intro_deeplearning.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/articles/intro_deeplearning.pdf -------------------------------------------------------------------------------- /articles/whataremotifs.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/articles/whataremotifs.pdf -------------------------------------------------------------------------------- /data/SNP/ASB.auto.v2.1.aug16.txt.tgz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/data/SNP/ASB.auto.v2.1.aug16.txt.tgz -------------------------------------------------------------------------------- /data/SNP/GSE31388_dsQtlTableLong.txt.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/data/SNP/GSE31388_dsQtlTableLong.txt.gz -------------------------------------------------------------------------------- /data/SNP/gwas_catalog_v1.0-associations_e100_r2021-01-29.tsv.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/data/SNP/gwas_catalog_v1.0-associations_e100_r2021-01-29.tsv.gz -------------------------------------------------------------------------------- /data/bed/CTCF_GM12878_hg19_4000_neg.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/data/bed/CTCF_GM12878_hg19_4000_neg.bed -------------------------------------------------------------------------------- /data/bed/CTCF_GM12878_hg19_4000_pos.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/data/bed/CTCF_GM12878_hg19_4000_pos.bed -------------------------------------------------------------------------------- /data/bed/DNase_GM12878_hg19_4000_neg.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/data/bed/DNase_GM12878_hg19_4000_neg.bed -------------------------------------------------------------------------------- /data/bed/DNase_GM12878_hg19_4000_pos.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/data/bed/DNase_GM12878_hg19_4000_pos.bed -------------------------------------------------------------------------------- /data/bed/DSBCapture_NHEK_hg19_4000_neg.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/data/bed/DSBCapture_NHEK_hg19_4000_neg.bed -------------------------------------------------------------------------------- /data/bed/DSBCapture_NHEK_hg19_4000_pos.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/data/bed/DSBCapture_NHEK_hg19_4000_pos.bed -------------------------------------------------------------------------------- /data/bed/H3K4me3_GM12878_hg19_4000_neg.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/data/bed/H3K4me3_GM12878_hg19_4000_neg.bed -------------------------------------------------------------------------------- /data/bed/H3K4me3_GM12878_hg19_4000_pos.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/data/bed/H3K4me3_GM12878_hg19_4000_pos.bed -------------------------------------------------------------------------------- /data/bed/POL2_GM12878_hg19_4000_neg.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/data/bed/POL2_GM12878_hg19_4000_neg.bed -------------------------------------------------------------------------------- /data/bed/POL2_GM12878_hg19_4000_pos.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/data/bed/POL2_GM12878_hg19_4000_pos.bed -------------------------------------------------------------------------------- /data/fasta/CTCF_GM12878_hg19_4000_neg.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/data/fasta/CTCF_GM12878_hg19_4000_neg.fa -------------------------------------------------------------------------------- /data/fasta/CTCF_GM12878_hg19_4000_pos.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/data/fasta/CTCF_GM12878_hg19_4000_pos.fa -------------------------------------------------------------------------------- /data/fasta/DNase_GM12878_hg19_4000_neg.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/data/fasta/DNase_GM12878_hg19_4000_neg.fa -------------------------------------------------------------------------------- /data/fasta/DNase_GM12878_hg19_4000_pos.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/data/fasta/DNase_GM12878_hg19_4000_pos.fa -------------------------------------------------------------------------------- /data/fasta/DSBCapture_NHEK_hg19_4000_neg.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/data/fasta/DSBCapture_NHEK_hg19_4000_neg.fa -------------------------------------------------------------------------------- /data/fasta/DSBCapture_NHEK_hg19_4000_pos.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/data/fasta/DSBCapture_NHEK_hg19_4000_pos.fa -------------------------------------------------------------------------------- /data/fasta/H3K4me3_GM12878_hg19_4000_neg.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/data/fasta/H3K4me3_GM12878_hg19_4000_neg.fa -------------------------------------------------------------------------------- /data/fasta/H3K4me3_GM12878_hg19_4000_pos.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/data/fasta/H3K4me3_GM12878_hg19_4000_pos.fa -------------------------------------------------------------------------------- /data/fasta/POL2_GM12878_hg19_4000_neg.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/data/fasta/POL2_GM12878_hg19_4000_neg.fa -------------------------------------------------------------------------------- /data/fasta/POL2_GM12878_hg19_4000_pos.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/data/fasta/POL2_GM12878_hg19_4000_pos.fa -------------------------------------------------------------------------------- /data/fasta/sequences_SNPalt_hg19.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/data/fasta/sequences_SNPalt_hg19.fa -------------------------------------------------------------------------------- /data/fasta/sequences_SNPref_hg19.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/data/fasta/sequences_SNPref_hg19.fa -------------------------------------------------------------------------------- /data/narrowPeak/CTCF_GM12878_hg19.narrowPeak: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/data/narrowPeak/CTCF_GM12878_hg19.narrowPeak -------------------------------------------------------------------------------- /data/narrowPeak/DNase_GM12878_hg19.narrowPeak: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/data/narrowPeak/DNase_GM12878_hg19.narrowPeak -------------------------------------------------------------------------------- /data/narrowPeak/DSBCapture_NHEK_hg19.narrowPeak: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/data/narrowPeak/DSBCapture_NHEK_hg19.narrowPeak -------------------------------------------------------------------------------- /data/narrowPeak/H3K4me3_GM12878_hg19.narrowPeak: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/data/narrowPeak/H3K4me3_GM12878_hg19.narrowPeak -------------------------------------------------------------------------------- /data/narrowPeak/JUND_GM12878_hg19.narrowPeak: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/data/narrowPeak/JUND_GM12878_hg19.narrowPeak -------------------------------------------------------------------------------- /data/narrowPeak/P300_GM12878_hg19.narrowPeak: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/data/narrowPeak/P300_GM12878_hg19.narrowPeak -------------------------------------------------------------------------------- /data/narrowPeak/POL2_GM12878_hg19.narrowPeak: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/data/narrowPeak/POL2_GM12878_hg19.narrowPeak -------------------------------------------------------------------------------- /header_googlesites.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/header_googlesites.png -------------------------------------------------------------------------------- /results/SNP/mutationMap_201b_DNase.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/results/SNP/mutationMap_201b_DNase.pdf -------------------------------------------------------------------------------- /results/SNP/mutationMap_41b_DNase.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/results/SNP/mutationMap_41b_DNase.pdf -------------------------------------------------------------------------------- /results/model/CNN1_model_CTCF.hdf5: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/results/model/CNN1_model_CTCF.hdf5 -------------------------------------------------------------------------------- /results/model/CNN1_model_DNase.hdf5: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/results/model/CNN1_model_DNase.hdf5 -------------------------------------------------------------------------------- /results/model/CNN1_model_H3K4me3.hdf5: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/results/model/CNN1_model_H3K4me3.hdf5 -------------------------------------------------------------------------------- /results/model/CNN1_model_POL2.hdf5: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/results/model/CNN1_model_POL2.hdf5 -------------------------------------------------------------------------------- /results/motif/root_motifs_DNase.tf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/results/motif/root_motifs_DNase.tf -------------------------------------------------------------------------------- /results/motif/trimmed_redundant_motifs_CTCF.tf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/results/motif/trimmed_redundant_motifs_CTCF.tf -------------------------------------------------------------------------------- /results/motif/trimmed_redundant_motifs_DNase.tf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/results/motif/trimmed_redundant_motifs_DNase.tf -------------------------------------------------------------------------------- /results/motif/trimmed_redundant_motifs_H3K4me3.tf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/results/motif/trimmed_redundant_motifs_H3K4me3.tf -------------------------------------------------------------------------------- /results/motif/trimmed_redundant_motifs_POL2.tf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphaelmourad/CNN-for-genomics-training/HEAD/results/motif/trimmed_redundant_motifs_POL2.tf --------------------------------------------------------------------------------