CpGtools Documentation
Data Format
Test and Demo Datasets
Usage Information
Compare Differential Analysis Tools
Test dataset can be downloaded from this link
Reference gene model files can be downloaded from this link
pre-built TSV file used to annotate CpG according to its 450K/850K probe ID. MethylationEPIC_CpGtools.tsv.gz BED files uesd to annotate CpG according to its genomic positions (hg19/GRCh37) hg19_ENCODE_338TF_130Cell_E3.bed.gz hg19_ENCODE_DNaseI_125Cells_V3.bed.gz hg19_ENCODE_H3K27ac_11_cellLines_ChIP.bed.gz hg19_ENCODE_H3K4me1_11_cellLines_ChIP.bed.gz hg19_ENCODE_H3K4me3_11_cellLines_ChIP.bed.gz hg19_ENCODE_chromHMM_states_9Cells.merge.bed.gz hg19_FANTOM_enhancers_phase_1_and_2.bed.gz BED files uesd to annotate CpG according to its genomic positions (hg38/GRCh38) hg38_ENCODE_338TF_130Cell_E3.bed.gz hg38_ENCODE_DNaseI_125Cells_V3.bed.gz hg38_ENCODE_H3K27ac_11_cellLines_ChIP.bed.gz hg38_ENCODE_H3K4me1_11_cellLines_ChIP.bed.gz hg38_ENCODE_H3K4me3_11_cellLines_ChIP.bed.gz hg38_ENCODE_chromHMM_states_9Cells.merge.bed.gz hg38_FANTOM_enhancers_phase_1_and_2.bed.gz
pre-built TSV file used to annotate CpG according to its 450K/850K probe ID.
MethylationEPIC_CpGtools.tsv.gz
BED files uesd to annotate CpG according to its genomic positions (hg19/GRCh37)
hg19_ENCODE_338TF_130Cell_E3.bed.gz hg19_ENCODE_DNaseI_125Cells_V3.bed.gz hg19_ENCODE_H3K27ac_11_cellLines_ChIP.bed.gz hg19_ENCODE_H3K4me1_11_cellLines_ChIP.bed.gz hg19_ENCODE_H3K4me3_11_cellLines_ChIP.bed.gz hg19_ENCODE_chromHMM_states_9Cells.merge.bed.gz hg19_FANTOM_enhancers_phase_1_and_2.bed.gz
hg19_ENCODE_338TF_130Cell_E3.bed.gz
hg19_ENCODE_DNaseI_125Cells_V3.bed.gz
hg19_ENCODE_H3K27ac_11_cellLines_ChIP.bed.gz
hg19_ENCODE_H3K4me1_11_cellLines_ChIP.bed.gz
hg19_ENCODE_H3K4me3_11_cellLines_ChIP.bed.gz
hg19_ENCODE_chromHMM_states_9Cells.merge.bed.gz
hg19_FANTOM_enhancers_phase_1_and_2.bed.gz
BED files uesd to annotate CpG according to its genomic positions (hg38/GRCh38)
hg38_ENCODE_338TF_130Cell_E3.bed.gz hg38_ENCODE_DNaseI_125Cells_V3.bed.gz hg38_ENCODE_H3K27ac_11_cellLines_ChIP.bed.gz hg38_ENCODE_H3K4me1_11_cellLines_ChIP.bed.gz hg38_ENCODE_H3K4me3_11_cellLines_ChIP.bed.gz hg38_ENCODE_chromHMM_states_9Cells.merge.bed.gz hg38_FANTOM_enhancers_phase_1_and_2.bed.gz
hg38_ENCODE_338TF_130Cell_E3.bed.gz
hg38_ENCODE_DNaseI_125Cells_V3.bed.gz
hg38_ENCODE_H3K27ac_11_cellLines_ChIP.bed.gz
hg38_ENCODE_H3K4me1_11_cellLines_ChIP.bed.gz
hg38_ENCODE_H3K4me3_11_cellLines_ChIP.bed.gz
hg38_ENCODE_chromHMM_states_9Cells.merge.bed.gz
hg38_FANTOM_enhancers_phase_1_and_2.bed.gz