├── .gitignore ├── README.md ├── archive └── AIAP_v1.00 │ ├── AIAP_v1.00 │ ├── ATAC_IAP_v1.00.sh │ ├── DOR_analysis.R │ ├── DOR_analysis.sh │ ├── Dockerfile │ ├── qc_source.sh │ ├── visualization_local.R │ └── visualization_target.R │ ├── IFR_README.md │ ├── Usage.md │ ├── pipe_v1.2 │ ├── atac_v1.2.sh │ ├── find_image_ID_digest.sh │ ├── promoter_bin.py │ ├── qc_source.sh │ ├── random_chr.py │ ├── rpkm_bin.py │ └── visualization.R │ ├── target_collection │ └── atac_181018.sh │ ├── v1.2b │ ├── atac_v1.2b.sh │ ├── find_image_ID_digest.sh │ ├── promoter_bin.py │ ├── qc_source.sh │ ├── random_chr.py │ ├── rpkm_bin.py │ └── visualization.R │ └── v3.1 │ ├── atac_v3.1.sh │ ├── atac_v3.1b.sh │ ├── nochrm_atac_v3.1b.sh │ └── update_v3.1.sh ├── atac_ref ├── mm10_encode_pe │ ├── encode_pe.json │ ├── merged_background.txt │ ├── merged_bg_dichoto.txt │ ├── merged_bin_result.txt │ ├── merged_chrom_count.txt │ ├── merged_coding_promoter_peak_enrichment.txt │ ├── merged_dedup_percentage.txt │ ├── merged_dup_level.txt │ ├── merged_mapping_status.txt │ ├── merged_promoter_percentage.txt │ ├── merged_qc_summary.txt │ ├── merged_saturation_collection.txt │ ├── merged_sub10M_enrichment.txt │ ├── merged_unique_chrM_ratio.txt │ ├── merged_useful_reads.txt │ ├── readme.md │ └── temp │ │ └── merged_mapping_status.txt └── old_mm10_encode_pe │ ├── encode_pe.json │ ├── merged_background.txt │ ├── merged_bg_dichoto.txt │ ├── merged_chrom_count.txt │ ├── merged_coding_promoter_peak_enrichment.txt │ ├── merged_dedup_percentage.txt │ ├── merged_mapping_status.txt │ ├── merged_removed_reads.txt │ ├── merged_saturation_collection.txt │ ├── merged_sub10M_enrichment.txt │ ├── merged_uniq_chrM.txt │ ├── merged_useful_reads.txt │ ├── readme.md │ └── store │ └── merged_mapping_status.txt ├── documents ├── Documentation.md ├── ifr_documentation.md └── update_log.md ├── image_build_file ├── Dockerfile_base_AIAP_v1.1 └── simg_AIAP.def ├── pipe_code ├── .DS_Store ├── ATAC-seq_wellington.R ├── ATAC_IAP_v1.1.sh ├── DOR_analysis.R ├── DOR_analysis.sh ├── batch_result_collection.sh ├── find_image_ID_digest.sh ├── promoter_bin.py ├── qc_source.sh ├── random_chr.py ├── rpkm_bin.py └── visualization.R ├── pipe_code_AIAP ├── ATAC-seq_wellington.R ├── ATAC_IAP_v1.00.sh ├── DOR_analysis.R ├── DOR_analysis.sh ├── batch_result_collection.sh ├── find_image_ID_digest.sh ├── promoter_bin.py ├── qc_source.sh ├── random_chr.py ├── readme.txt ├── rpkm_bin.py └── visualization.R └── pipe_code_TaRGET_local ├── ATAC-seq_wellington.R ├── DOR_analysis.R ├── DOR_analysis.sh ├── atac_pipe_TaRGET.sh ├── batch_result_collection.sh ├── find_image_ID_digest.sh ├── promoter_bin.py ├── qc_source.sh ├── random_chr.py ├── readme.txt ├── rpkm_bin.py └── visualization.R /.gitignore: -------------------------------------------------------------------------------- 1 | .DS_Store 2 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/README.md -------------------------------------------------------------------------------- /archive/AIAP_v1.00/AIAP_v1.00/ATAC_IAP_v1.00.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/archive/AIAP_v1.00/AIAP_v1.00/ATAC_IAP_v1.00.sh -------------------------------------------------------------------------------- /archive/AIAP_v1.00/AIAP_v1.00/DOR_analysis.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/archive/AIAP_v1.00/AIAP_v1.00/DOR_analysis.R -------------------------------------------------------------------------------- /archive/AIAP_v1.00/AIAP_v1.00/DOR_analysis.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/archive/AIAP_v1.00/AIAP_v1.00/DOR_analysis.sh -------------------------------------------------------------------------------- /archive/AIAP_v1.00/AIAP_v1.00/Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/archive/AIAP_v1.00/AIAP_v1.00/Dockerfile -------------------------------------------------------------------------------- /archive/AIAP_v1.00/AIAP_v1.00/qc_source.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/archive/AIAP_v1.00/AIAP_v1.00/qc_source.sh -------------------------------------------------------------------------------- /archive/AIAP_v1.00/AIAP_v1.00/visualization_local.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/archive/AIAP_v1.00/AIAP_v1.00/visualization_local.R -------------------------------------------------------------------------------- /archive/AIAP_v1.00/AIAP_v1.00/visualization_target.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/archive/AIAP_v1.00/AIAP_v1.00/visualization_target.R -------------------------------------------------------------------------------- /archive/AIAP_v1.00/IFR_README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/archive/AIAP_v1.00/IFR_README.md -------------------------------------------------------------------------------- /archive/AIAP_v1.00/Usage.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/archive/AIAP_v1.00/Usage.md -------------------------------------------------------------------------------- /archive/AIAP_v1.00/pipe_v1.2/atac_v1.2.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/archive/AIAP_v1.00/pipe_v1.2/atac_v1.2.sh -------------------------------------------------------------------------------- /archive/AIAP_v1.00/pipe_v1.2/find_image_ID_digest.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/archive/AIAP_v1.00/pipe_v1.2/find_image_ID_digest.sh -------------------------------------------------------------------------------- /archive/AIAP_v1.00/pipe_v1.2/promoter_bin.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/archive/AIAP_v1.00/pipe_v1.2/promoter_bin.py -------------------------------------------------------------------------------- /archive/AIAP_v1.00/pipe_v1.2/qc_source.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/archive/AIAP_v1.00/pipe_v1.2/qc_source.sh -------------------------------------------------------------------------------- /archive/AIAP_v1.00/pipe_v1.2/random_chr.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/archive/AIAP_v1.00/pipe_v1.2/random_chr.py -------------------------------------------------------------------------------- /archive/AIAP_v1.00/pipe_v1.2/rpkm_bin.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/archive/AIAP_v1.00/pipe_v1.2/rpkm_bin.py -------------------------------------------------------------------------------- /archive/AIAP_v1.00/pipe_v1.2/visualization.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/archive/AIAP_v1.00/pipe_v1.2/visualization.R -------------------------------------------------------------------------------- /archive/AIAP_v1.00/target_collection/atac_181018.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/archive/AIAP_v1.00/target_collection/atac_181018.sh -------------------------------------------------------------------------------- /archive/AIAP_v1.00/v1.2b/atac_v1.2b.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/archive/AIAP_v1.00/v1.2b/atac_v1.2b.sh -------------------------------------------------------------------------------- /archive/AIAP_v1.00/v1.2b/find_image_ID_digest.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/archive/AIAP_v1.00/v1.2b/find_image_ID_digest.sh -------------------------------------------------------------------------------- /archive/AIAP_v1.00/v1.2b/promoter_bin.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/archive/AIAP_v1.00/v1.2b/promoter_bin.py -------------------------------------------------------------------------------- /archive/AIAP_v1.00/v1.2b/qc_source.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/archive/AIAP_v1.00/v1.2b/qc_source.sh -------------------------------------------------------------------------------- /archive/AIAP_v1.00/v1.2b/random_chr.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/archive/AIAP_v1.00/v1.2b/random_chr.py -------------------------------------------------------------------------------- /archive/AIAP_v1.00/v1.2b/rpkm_bin.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/archive/AIAP_v1.00/v1.2b/rpkm_bin.py -------------------------------------------------------------------------------- /archive/AIAP_v1.00/v1.2b/visualization.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/archive/AIAP_v1.00/v1.2b/visualization.R -------------------------------------------------------------------------------- /archive/AIAP_v1.00/v3.1/atac_v3.1.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/archive/AIAP_v1.00/v3.1/atac_v3.1.sh -------------------------------------------------------------------------------- /archive/AIAP_v1.00/v3.1/atac_v3.1b.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/archive/AIAP_v1.00/v3.1/atac_v3.1b.sh -------------------------------------------------------------------------------- /archive/AIAP_v1.00/v3.1/nochrm_atac_v3.1b.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/archive/AIAP_v1.00/v3.1/nochrm_atac_v3.1b.sh -------------------------------------------------------------------------------- /archive/AIAP_v1.00/v3.1/update_v3.1.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/archive/AIAP_v1.00/v3.1/update_v3.1.sh -------------------------------------------------------------------------------- /atac_ref/mm10_encode_pe/encode_pe.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/atac_ref/mm10_encode_pe/encode_pe.json -------------------------------------------------------------------------------- /atac_ref/mm10_encode_pe/merged_background.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/atac_ref/mm10_encode_pe/merged_background.txt -------------------------------------------------------------------------------- /atac_ref/mm10_encode_pe/merged_bg_dichoto.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/atac_ref/mm10_encode_pe/merged_bg_dichoto.txt -------------------------------------------------------------------------------- /atac_ref/mm10_encode_pe/merged_bin_result.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/atac_ref/mm10_encode_pe/merged_bin_result.txt -------------------------------------------------------------------------------- /atac_ref/mm10_encode_pe/merged_chrom_count.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/atac_ref/mm10_encode_pe/merged_chrom_count.txt -------------------------------------------------------------------------------- /atac_ref/mm10_encode_pe/merged_coding_promoter_peak_enrichment.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/atac_ref/mm10_encode_pe/merged_coding_promoter_peak_enrichment.txt -------------------------------------------------------------------------------- /atac_ref/mm10_encode_pe/merged_dedup_percentage.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/atac_ref/mm10_encode_pe/merged_dedup_percentage.txt -------------------------------------------------------------------------------- /atac_ref/mm10_encode_pe/merged_dup_level.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/atac_ref/mm10_encode_pe/merged_dup_level.txt -------------------------------------------------------------------------------- /atac_ref/mm10_encode_pe/merged_mapping_status.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/atac_ref/mm10_encode_pe/merged_mapping_status.txt -------------------------------------------------------------------------------- /atac_ref/mm10_encode_pe/merged_promoter_percentage.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/atac_ref/mm10_encode_pe/merged_promoter_percentage.txt -------------------------------------------------------------------------------- /atac_ref/mm10_encode_pe/merged_qc_summary.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/atac_ref/mm10_encode_pe/merged_qc_summary.txt -------------------------------------------------------------------------------- /atac_ref/mm10_encode_pe/merged_saturation_collection.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/atac_ref/mm10_encode_pe/merged_saturation_collection.txt -------------------------------------------------------------------------------- /atac_ref/mm10_encode_pe/merged_sub10M_enrichment.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/atac_ref/mm10_encode_pe/merged_sub10M_enrichment.txt -------------------------------------------------------------------------------- /atac_ref/mm10_encode_pe/merged_unique_chrM_ratio.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/atac_ref/mm10_encode_pe/merged_unique_chrM_ratio.txt -------------------------------------------------------------------------------- /atac_ref/mm10_encode_pe/merged_useful_reads.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/atac_ref/mm10_encode_pe/merged_useful_reads.txt -------------------------------------------------------------------------------- /atac_ref/mm10_encode_pe/readme.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/atac_ref/mm10_encode_pe/readme.md -------------------------------------------------------------------------------- /atac_ref/mm10_encode_pe/temp/merged_mapping_status.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/atac_ref/mm10_encode_pe/temp/merged_mapping_status.txt -------------------------------------------------------------------------------- /atac_ref/old_mm10_encode_pe/encode_pe.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/atac_ref/old_mm10_encode_pe/encode_pe.json -------------------------------------------------------------------------------- /atac_ref/old_mm10_encode_pe/merged_background.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/atac_ref/old_mm10_encode_pe/merged_background.txt -------------------------------------------------------------------------------- /atac_ref/old_mm10_encode_pe/merged_bg_dichoto.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/atac_ref/old_mm10_encode_pe/merged_bg_dichoto.txt -------------------------------------------------------------------------------- /atac_ref/old_mm10_encode_pe/merged_chrom_count.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/atac_ref/old_mm10_encode_pe/merged_chrom_count.txt -------------------------------------------------------------------------------- /atac_ref/old_mm10_encode_pe/merged_coding_promoter_peak_enrichment.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/atac_ref/old_mm10_encode_pe/merged_coding_promoter_peak_enrichment.txt -------------------------------------------------------------------------------- /atac_ref/old_mm10_encode_pe/merged_dedup_percentage.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/atac_ref/old_mm10_encode_pe/merged_dedup_percentage.txt -------------------------------------------------------------------------------- /atac_ref/old_mm10_encode_pe/merged_mapping_status.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/atac_ref/old_mm10_encode_pe/merged_mapping_status.txt -------------------------------------------------------------------------------- /atac_ref/old_mm10_encode_pe/merged_removed_reads.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/atac_ref/old_mm10_encode_pe/merged_removed_reads.txt -------------------------------------------------------------------------------- /atac_ref/old_mm10_encode_pe/merged_saturation_collection.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/atac_ref/old_mm10_encode_pe/merged_saturation_collection.txt -------------------------------------------------------------------------------- /atac_ref/old_mm10_encode_pe/merged_sub10M_enrichment.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/atac_ref/old_mm10_encode_pe/merged_sub10M_enrichment.txt -------------------------------------------------------------------------------- /atac_ref/old_mm10_encode_pe/merged_uniq_chrM.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/atac_ref/old_mm10_encode_pe/merged_uniq_chrM.txt -------------------------------------------------------------------------------- /atac_ref/old_mm10_encode_pe/merged_useful_reads.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/atac_ref/old_mm10_encode_pe/merged_useful_reads.txt -------------------------------------------------------------------------------- /atac_ref/old_mm10_encode_pe/readme.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/atac_ref/old_mm10_encode_pe/readme.md -------------------------------------------------------------------------------- /atac_ref/old_mm10_encode_pe/store/merged_mapping_status.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/atac_ref/old_mm10_encode_pe/store/merged_mapping_status.txt -------------------------------------------------------------------------------- /documents/Documentation.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/documents/Documentation.md -------------------------------------------------------------------------------- /documents/ifr_documentation.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/documents/ifr_documentation.md -------------------------------------------------------------------------------- /documents/update_log.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/documents/update_log.md -------------------------------------------------------------------------------- /image_build_file/Dockerfile_base_AIAP_v1.1: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/image_build_file/Dockerfile_base_AIAP_v1.1 -------------------------------------------------------------------------------- /image_build_file/simg_AIAP.def: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/image_build_file/simg_AIAP.def -------------------------------------------------------------------------------- /pipe_code/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/pipe_code/.DS_Store -------------------------------------------------------------------------------- /pipe_code/ATAC-seq_wellington.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/pipe_code/ATAC-seq_wellington.R -------------------------------------------------------------------------------- /pipe_code/ATAC_IAP_v1.1.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/pipe_code/ATAC_IAP_v1.1.sh -------------------------------------------------------------------------------- /pipe_code/DOR_analysis.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/pipe_code/DOR_analysis.R -------------------------------------------------------------------------------- /pipe_code/DOR_analysis.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/pipe_code/DOR_analysis.sh -------------------------------------------------------------------------------- /pipe_code/batch_result_collection.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/pipe_code/batch_result_collection.sh -------------------------------------------------------------------------------- /pipe_code/find_image_ID_digest.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/pipe_code/find_image_ID_digest.sh -------------------------------------------------------------------------------- /pipe_code/promoter_bin.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/pipe_code/promoter_bin.py -------------------------------------------------------------------------------- /pipe_code/qc_source.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/pipe_code/qc_source.sh -------------------------------------------------------------------------------- /pipe_code/random_chr.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/pipe_code/random_chr.py -------------------------------------------------------------------------------- /pipe_code/rpkm_bin.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/pipe_code/rpkm_bin.py -------------------------------------------------------------------------------- /pipe_code/visualization.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/pipe_code/visualization.R -------------------------------------------------------------------------------- /pipe_code_AIAP/ATAC-seq_wellington.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/pipe_code_AIAP/ATAC-seq_wellington.R -------------------------------------------------------------------------------- /pipe_code_AIAP/ATAC_IAP_v1.00.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/pipe_code_AIAP/ATAC_IAP_v1.00.sh -------------------------------------------------------------------------------- /pipe_code_AIAP/DOR_analysis.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/pipe_code_AIAP/DOR_analysis.R -------------------------------------------------------------------------------- /pipe_code_AIAP/DOR_analysis.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/pipe_code_AIAP/DOR_analysis.sh -------------------------------------------------------------------------------- /pipe_code_AIAP/batch_result_collection.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/pipe_code_AIAP/batch_result_collection.sh -------------------------------------------------------------------------------- /pipe_code_AIAP/find_image_ID_digest.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/pipe_code_AIAP/find_image_ID_digest.sh -------------------------------------------------------------------------------- /pipe_code_AIAP/promoter_bin.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/pipe_code_AIAP/promoter_bin.py -------------------------------------------------------------------------------- /pipe_code_AIAP/qc_source.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/pipe_code_AIAP/qc_source.sh -------------------------------------------------------------------------------- /pipe_code_AIAP/random_chr.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/pipe_code_AIAP/random_chr.py -------------------------------------------------------------------------------- /pipe_code_AIAP/readme.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/pipe_code_AIAP/readme.txt -------------------------------------------------------------------------------- /pipe_code_AIAP/rpkm_bin.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/pipe_code_AIAP/rpkm_bin.py -------------------------------------------------------------------------------- /pipe_code_AIAP/visualization.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/pipe_code_AIAP/visualization.R -------------------------------------------------------------------------------- /pipe_code_TaRGET_local/ATAC-seq_wellington.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/pipe_code_TaRGET_local/ATAC-seq_wellington.R -------------------------------------------------------------------------------- /pipe_code_TaRGET_local/DOR_analysis.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/pipe_code_TaRGET_local/DOR_analysis.R -------------------------------------------------------------------------------- /pipe_code_TaRGET_local/DOR_analysis.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/pipe_code_TaRGET_local/DOR_analysis.sh -------------------------------------------------------------------------------- /pipe_code_TaRGET_local/atac_pipe_TaRGET.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/pipe_code_TaRGET_local/atac_pipe_TaRGET.sh -------------------------------------------------------------------------------- /pipe_code_TaRGET_local/batch_result_collection.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/pipe_code_TaRGET_local/batch_result_collection.sh -------------------------------------------------------------------------------- /pipe_code_TaRGET_local/find_image_ID_digest.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/pipe_code_TaRGET_local/find_image_ID_digest.sh -------------------------------------------------------------------------------- /pipe_code_TaRGET_local/promoter_bin.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/pipe_code_TaRGET_local/promoter_bin.py -------------------------------------------------------------------------------- /pipe_code_TaRGET_local/qc_source.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/pipe_code_TaRGET_local/qc_source.sh -------------------------------------------------------------------------------- /pipe_code_TaRGET_local/random_chr.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/pipe_code_TaRGET_local/random_chr.py -------------------------------------------------------------------------------- /pipe_code_TaRGET_local/readme.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/pipe_code_TaRGET_local/readme.txt -------------------------------------------------------------------------------- /pipe_code_TaRGET_local/rpkm_bin.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/pipe_code_TaRGET_local/rpkm_bin.py -------------------------------------------------------------------------------- /pipe_code_TaRGET_local/visualization.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Zhang-lab/ATAC-seq_QC_analysis/HEAD/pipe_code_TaRGET_local/visualization.R --------------------------------------------------------------------------------