2021-08-19 v3.3 * Fixed the format of TATA-box annotation 2021-07-21 v3.2 * Updated TSS annotation * Updated TATA-box annotation * Updated HOMER annotation * Added R data format (RDS) file 2019-04-20 v3.1 * Updated TSS annotation * Updated Regulatory Build annotation * Add center positions of TSS regoins in the coordination files 2018-12-31 v3.0 * Removed unnecessary and problematic samples in the source data, and rebuilt an integrated TSS peak set (human) * Revised analysis results based on the above rebuild TSS peak set * Removed CNE results * Added Regulatory build analysis result * Revised annotation based on the latest annotation sources 2018-02-22 v2.1 human/ change file name and compress files refTSS_v2.1_human_annotation.txt --> refTSS_v2.1_human_annotation.txt.gz refTSS_v2.1_human_coordinate.hg38.bed --> refTSS_v2.1_human_coordinate.hg38.bed.gz refTSS_v2.1_human_transcript.txt --> refTSS_v2.1_human_transcript.txt.gz cne/ hg38_mm10_CNE_annotation.tab --> hg38_mm10_CNE_annotation.txt.gz conservation/ liftovered_mm10_to_hg38_peaks_overlapped_reftss_hg38_500bp.bed --> liftovered_mm10_to_hg38_peaks_overlapped_reftss_hg38_500bp.bed.gz reftss_hg38_peaks_overlapped_liftovered_mm10_to_hg38_500bp.bed --> reftss_hg38_peaks_overlapped_liftovered_mm10_to_hg38_500bp.bed.gz sources/ DRA000914_hg38_CAGE_paraclu_output_mv99_simplified_L20.bed --> DRA000914_hg38_CAGE_paraclu_output_mv99_simplified_L20.bed.gz ENCODE_CAGE_paraclu_output_mv1412_simplified_L20.bed --> ENCODE_CAGE_paraclu_output_mv1412_simplified_L20.bed.gz Hs_EPDnew_004_hg38.one.bed --> Hs_EPDnew_004_hg38.one.bed.gz dbtss_paraclu_output_mv464_simplified_L20.bed --> dbtss_paraclu_output_mv464_simplified_L20.bed.gz hg38_v3.CAGE_peaks_merged.bed --> hg38_v3.CAGE_peaks_merged.bed.gz rampge_paraclu_output_mv17233_simplified_L20.bed --> rampge_paraclu_output_mv17233_simplified_L20.bed.gz tata_box_annotations/ hg38_tata_annotation_V2.txt --> hg38_tata_annotation_V2.txt.gz reftss.hg38.basic.homer.annotations.txt --> reftss.hg38.basic.homer.annotations.txt.gz add files tss_classification/TSS.classification.hg38.txt.gz change fileheader refTSS_v2.1_human_annotation.txt.gz refTSS_v2.1_human_coordinate.hg38.bed.gz refTSS_v2.1_human_transcript.txt.gz tata_box_annotations/ hg38_tata_annotation_V2.txt.gz reftss.hg38.basic.homer.annotations.txt.gz mouse/ same as "human/"