Pre-compiled datasets
======================

Test datasets
-------------
Test dataset can be downloaded from `this link <https://sourceforge.net/projects/cpgtools/files/test/>`_

Reference gene models
---------------------
Reference gene model files can be downloaded from `this link <https://sourceforge.net/projects/cpgtools/files/refgene/>`_

Annotation datasets
--------------------

 - pre-built TSV file used to annotate CpG according to its 450K/850K probe ID. 
  
  * `MethylationEPIC_CpGtools.tsv.gz <https://sourceforge.net/projects/cpgtools/files/data/MethylationEPIC_CpGtools.tsv.gz/download>`_

 - BED files used to annotate CpG according to its genomic positions (hg19/GRCh37)
  
  * `hg19_ENCODE_338TF_130Cell_E3.bed.gz <https://sourceforge.net/projects/cpgtools/files/data/hg19_ENCODE_338TF_130Cell_E3.bed.gz/download>`_
  * `hg19_ENCODE_DNaseI_125Cells_V3.bed.gz <https://sourceforge.net/projects/cpgtools/files/data/hg19_ENCODE_DNaseI_125Cells_V3.bed.gz/download>`_
  * `hg19_ENCODE_H3K27ac_11_cellLines_ChIP.bed.gz <https://sourceforge.net/projects/cpgtools/files/data/hg19_ENCODE_H3K27ac_11_cellLines_ChIP.bed.gz/download>`_
  * `hg19_ENCODE_H3K4me1_11_cellLines_ChIP.bed.gz <https://sourceforge.net/projects/cpgtools/files/data/hg19_ENCODE_H3K4me1_11_cellLines_ChIP.bed.gz/download>`_
  * `hg19_ENCODE_H3K4me3_11_cellLines_ChIP.bed.gz <https://sourceforge.net/projects/cpgtools/files/data/hg19_ENCODE_H3K4me3_11_cellLines_ChIP.bed.gz/download>`_
  * `hg19_ENCODE_chromHMM_states_9Cells.merge.bed.gz <https://sourceforge.net/projects/cpgtools/files/data/hg19_ENCODE_chromHMM_states_9Cells.merge.bed.gz/download>`_
  * `hg19_FANTOM_enhancers_phase_1_and_2.bed.gz <https://sourceforge.net/projects/cpgtools/files/data/hg19_FANTOM_enhancers_phase_1_and_2.bed.gz/download>`_

 - BED files used to annotate CpG according to its genomic locations (hg38/GRCh38)
  
  *	`hg38_ENCODE_338TF_130Cell_E3.bed.gz <https://sourceforge.net/projects/cpgtools/files/data/hg38_ENCODE_338TF_130Cell_E3.bed.gz/download>`_
  * `hg38_ENCODE_DNaseI_125Cells_V3.bed.gz <https://sourceforge.net/projects/cpgtools/files/data/hg38_ENCODE_DNaseI_125Cells_V3.bed.gz/download>`_
  * `hg38_ENCODE_H3K27ac_11_cellLines_ChIP.bed.gz <https://sourceforge.net/projects/cpgtools/files/data/hg38_ENCODE_H3K27ac_11_cellLines_ChIP.bed.gz/download>`_
  * `hg38_ENCODE_H3K4me1_11_cellLines_ChIP.bed.gz <https://sourceforge.net/projects/cpgtools/files/data/hg38_ENCODE_H3K4me1_11_cellLines_ChIP.bed.gz/download>`_
  * `hg38_ENCODE_H3K4me3_11_cellLines_ChIP.bed.gz <https://sourceforge.net/projects/cpgtools/files/data/hg38_ENCODE_H3K4me3_11_cellLines_ChIP.bed.gz/download>`_
  * `hg38_ENCODE_chromHMM_states_9Cells.merge.bed.gz <https://sourceforge.net/projects/cpgtools/files/data/hg38_ENCODE_chromHMM_states_9Cells.merge.bed.gz/download>`_
  * `hg38_FANTOM_enhancers_phase_1_and_2.bed.gz <https://sourceforge.net/projects/cpgtools/files/data/hg38_FANTOM_enhancers_phase_1_and_2.bed.gz/download>`_
	
