Index of /kundaje/marinovg/oak/various/papers/2024_KAS-ATAC/2021-03-05-figures
Name
Last modified
Size
Description
Parent Directory
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2016-11-16-refFlat.genes.merged.bed
2024-04-29 20:24
494K
DESeq2/
2021-03-05 17:56
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E116_18_core_K27ac_hg38lift_dense.bed.gz
2018-03-31 03:11
5.4M
E116_18_core_K27ac_hg38lift_expanded.bed.gz
2018-03-31 03:12
2.3M
E116_18_core_K27ac_hg38lift_mnemonics.1_TssA
2021-03-05 19:29
725K
E116_18_core_K27ac_hg38lift_mnemonics.2_TssFlnk
2021-03-05 19:29
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E116_18_core_K27ac_hg38lift_mnemonics.3_TssFlnkU
2021-03-05 19:29
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E116_18_core_K27ac_hg38lift_mnemonics.4_TssFlnkD
2021-03-05 19:29
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E116_18_core_K27ac_hg38lift_mnemonics.5_Tx
2021-03-05 19:29
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E116_18_core_K27ac_hg38lift_mnemonics.6_TxWk
2021-03-05 19:29
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E116_18_core_K27ac_hg38lift_mnemonics.7_EnhG1
2021-03-05 19:29
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E116_18_core_K27ac_hg38lift_mnemonics.8_EnhG2
2021-03-05 19:29
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E116_18_core_K27ac_hg38lift_mnemonics.9_EnhA1
2021-03-05 19:29
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E116_18_core_K27ac_hg38lift_mnemonics.10_EnhA2
2021-03-05 19:29
316K
E116_18_core_K27ac_hg38lift_mnemonics.11_EnhWk
2021-03-05 19:29
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E116_18_core_K27ac_hg38lift_mnemonics.12_ZNF_Rpts
2021-03-05 19:29
1.0M
E116_18_core_K27ac_hg38lift_mnemonics.13_Het
2021-03-05 19:29
1.1M
E116_18_core_K27ac_hg38lift_mnemonics.14_TssBiv
2021-03-05 19:29
117K
E116_18_core_K27ac_hg38lift_mnemonics.15_EnhBiv
2021-03-05 19:29
133K
E116_18_core_K27ac_hg38lift_mnemonics.16_ReprPC
2021-03-05 19:29
321K
E116_18_core_K27ac_hg38lift_mnemonics.17_ReprPCWk
2021-03-05 19:29
1.0M
E116_18_core_K27ac_hg38lift_mnemonics.18_Quies
2021-03-05 19:29
1.9M
E116_18_core_K27ac_hg38lift_mnemonics.bed.gz
2018-03-31 03:12
3.3M
E116_18_core_K27ac_hg38lift_segments.bed.gz
2018-03-31 03:12
3.2M
E116_18_core_K27ac_hg38lift_stateno.bed.gz
2018-04-14 00:28
3.1M
E116_18_core_K27ac_hg38lift_stateno.bed.gz.tbi
2018-04-14 00:28
947K
ENCODE-TF-peaks/
2024-04-18 03:51
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FIMO-files/
2024-04-19 07:27
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FIMO-gzip.sh
2024-04-18 03:43
36K
FIMO-peaks-intersects.sh
2024-04-18 06:31
94K
FIMO-signal-around.sh
2024-04-18 04:07
653K
GM12878-CTCF-ENCFF827JRI-vs-TSS-500bp-intersection1.gz
2024-04-18 09:46
82K
GM12878-CTCF-ENCFF827JRI-vs-TSS-500bp-outersection1
2024-04-18 09:46
2.8M
GM12878-FIMO-CIS-BP-vs-G4-intersection1
2024-04-20 03:34
146K
GM12878-RAMPAGE-ENCSR000AEI.idr_peak-vs-2016-11-16-refFlat.TSS-500bp-intersection1.gz
2024-03-20 13:23
207K
GM12878-RAMPAGE-ENCSR000AEI.idr_peak-vs-2016-11-16-refFlat.TSS-500bp-intersection1_split.0.0
2024-03-20 13:27
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GM12878-RAMPAGE-ENCSR000AEI.idr_peak-vs-2016-11-16-refFlat.TSS-500bp-intersection1_split.100.0
2024-03-20 13:27
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GM12878-RAMPAGE-ENCSR000AEI.idr_peak-vs-2016-11-16-refFlat.TSS-500bp-intersection1_split.1000.0
2024-03-20 13:27
162K
GM12878-RAMPAGE-ENCSR000AEI.idr_peak-vs-2016-11-16-refFlat.TSS-500bp-outersection1_split.0.0
2024-03-20 13:27
108K
GM12878-RAMPAGE-ENCSR000AEI.idr_peak-vs-2016-11-16-refFlat.TSS-500bp-outersection1_split.100.0
2024-03-20 13:27
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GM12878-RAMPAGE-ENCSR000AEI.idr_peak-vs-2016-11-16-refFlat.TSS-500bp-outersection1_split.1000.0
2024-03-20 13:27
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GM12878-RAMPAGE-ENCSR000AEI.idr_peak.bed
2019-02-09 13:06
937K
GM12878-RAMPAGE-ENCSR000AEI.tss_peak-vs-2016-11-16-refFlat.TSS-500bp-intersection1.gz
2024-03-20 13:23
647K
GM12878-RAMPAGE-ENCSR000AEI.tss_peak-vs-2016-11-16-refFlat.TSS-500bp-intersection1_split.0.0
2024-03-20 13:27
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GM12878-RAMPAGE-ENCSR000AEI.tss_peak-vs-2016-11-16-refFlat.TSS-500bp-intersection1_split.100.0
2024-03-20 13:27
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GM12878-RAMPAGE-ENCSR000AEI.tss_peak-vs-2016-11-16-refFlat.TSS-500bp-intersection1_split.1000.0
2024-03-20 13:27
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GM12878-RAMPAGE-ENCSR000AEI.tss_peak-vs-2016-11-16-refFlat.TSS-500bp-outersection1_split.0.0
2024-03-20 13:27
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GM12878-RAMPAGE-ENCSR000AEI.tss_peak-vs-2016-11-16-refFlat.TSS-500bp-outersection1_split.100.0
2024-03-20 13:27
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GM12878-RAMPAGE-ENCSR000AEI.tss_peak-vs-2016-11-16-refFlat.TSS-500bp-outersection1_split.1000.0
2024-03-20 13:27
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GM12878-RAMPAGE-ENCSR000AEI.tsss_peak.bed
2019-02-09 13:05
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GM12878.KAS_ATAC_peaks.200bp_merge_200bp.RPM-vs-TSS-500bp-intersection1.gz
2024-04-18 09:34
266K
GM12878.KAS_ATAC_peaks.200bp_merge_200bp.RPM-vs-TSS-500bp-outersection1
2024-04-18 09:34
1.8M
GM12878.KAS_ATAC_peaks.200bp_merge_200bp.RPM.files
2021-03-05 17:02
748
GM12878.KAS_ATAC_peaks.200bp_merge_200bp.RPM.table
2021-03-05 17:05
2.9M
GM12878.KAS_ATAC_peaks.200bp_merge_200bp.RPM.table.bed
2024-04-18 09:24
2.9M
GM12878.KAS_ATAC_peaks.200bp_merge_200bp.SK-L007-GM12868-ATAC_50K_cells_5uM_Kethoxal_1x_PBS_wash_biotin_pulldown-1.RPM
2021-03-05 17:04
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GM12878.KAS_ATAC_peaks.200bp_merge_200bp.SK-L007-GM12868-ATAC_50K_cells_5uM_Kethoxal_1x_PBS_wash_biotin_pulldown-1.counts
2021-03-05 17:04
1.1M
GM12878.KAS_ATAC_peaks.200bp_merge_200bp.SK-L008-GM12868-ATAC_50K_cells_5uM_Kethoxal_1x_PBS_wash_biotin_pulldown-2.RPM
2021-03-05 17:04
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GM12878.KAS_ATAC_peaks.200bp_merge_200bp.SK-L008-GM12868-ATAC_50K_cells_5uM_Kethoxal_1x_PBS_wash_biotin_pulldown-2.counts
2021-03-05 17:04
1.1M
GM12878.KAS_ATAC_peaks.200bp_merge_200bp.SK-L009-GM12868-ATAC_50K_cells_5uM_Kethoxal_1x_PBS_wash_input-1.RPM
2021-03-05 17:04
1.4M
GM12878.KAS_ATAC_peaks.200bp_merge_200bp.SK-L009-GM12868-ATAC_50K_cells_5uM_Kethoxal_1x_PBS_wash_input-1.counts
2021-03-05 17:04
1.1M
GM12878.KAS_ATAC_peaks.200bp_merge_200bp.SK-L010-GM12868-ATAC_50K_cells_5uM_Kethoxal_1x_PBS_wash_input-2.RPM
2021-03-05 17:04
1.4M
GM12878.KAS_ATAC_peaks.200bp_merge_200bp.SK-L010-GM12868-ATAC_50K_cells_5uM_Kethoxal_1x_PBS_wash_input-2.counts
2021-03-05 17:04
1.1M
GM12878.KAS_ATAC_peaks.200bp_merge_200bp.counts.ATAC-vs-KAS-ATAC-vs-chroHMM
2021-03-06 01:15
33M
GM12878.KAS_ATAC_peaks.200bp_merge_200bp.counts.ATAC-vs-KAS-ATAC-vs-chroHMM-intersection2.hist
2024-03-20 12:03
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GM12878.KAS_ATAC_peaks.200bp_merge_200bp.counts.ATAC-vs-KAS-ATAC.p-adj-0.05-down-vs-chroHMM
2021-03-06 01:20
28M
GM12878.KAS_ATAC_peaks.200bp_merge_200bp.counts.ATAC-vs-KAS-ATAC.p-adj-0.05-down-vs-chroHMM-intersection2.hist
2024-03-20 12:03
0
GM12878.KAS_ATAC_peaks.200bp_merge_200bp.counts.ATAC-vs-KAS-ATAC.p-adj-0.05-up-vs-chroHMM
2021-03-06 02:12
29M
GM12878.KAS_ATAC_peaks.200bp_merge_200bp.counts.ATAC-vs-KAS-ATAC.p-adj-0.05-up-vs-chroHMM-intersection2.hist
2024-03-20 12:03
0
GM12878.KAS_ATAC_peaks.200bp_merge_200bp.counts.files
2021-03-05 17:02
760
GM12878.KAS_ATAC_peaks.200bp_merge_200bp.counts.table
2021-03-05 17:05
1.6M
GM12878.KAS_ATAC_peaks.200bp_merge_200bp.table
2021-03-05 16:55
1.2M
GM12878.KAS_ATAC_peaks.files
2021-03-05 16:53
1.4K
GSM3003539_Homo_all_w15_th-1_minus.hits.max.K.w50.25.bed.gz
2018-02-06 14:38
2.0M
GSM3003539_Homo_all_w15_th-1_minus_plus.hits.max.K.w50.25.bed
2024-04-19 03:17
12M
GSM3003539_Homo_all_w15_th-1_minus_plus.hits.max.K.w50.25.liftOver-vs-GM12878-peaks-intersection1.gz
2024-04-19 03:26
40K
GSM3003539_Homo_all_w15_th-1_minus_plus.hits.max.K.w50.25.liftOver-vs-GM12878-peaks-outersection1
2024-04-19 03:26
13M
GSM3003539_Homo_all_w15_th-1_minus_plus.hits.max.K.w50.25.liftOver-vs-HEK293-peaks-intersection1.gz
2024-04-19 03:26
46K
GSM3003539_Homo_all_w15_th-1_minus_plus.hits.max.K.w50.25.liftOver-vs-HEK293-peaks-outersection1
2024-04-19 03:26
13M
GSM3003539_Homo_all_w15_th-1_minus_plus.hits.max.K.w50.25.liftOver.bed
2024-04-19 03:24
13M
GSM3003539_Homo_all_w15_th-1_plus.hits.max.K.w50.25.bed.gz
2018-02-06 14:38
2.0M
GSM3003540_Homo_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.gz
2018-02-06 14:39
6.2M
GSM3003540_Homo_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.gz
2018-02-06 14:39
6.2M
HEK293-CTCF-ENCFF071FSR-vs-TSS-500bp-intersection1.gz
2024-04-18 09:46
79K
HEK293-CTCF-ENCFF071FSR-vs-TSS-500bp-outersection1
2024-04-18 09:46
2.8M
HEK293-CTCF-ENCFF071FSR-vs-TSS-500bp-outersection1-vs-genes-intersection1
2024-04-29 20:28
1.2M
HEK293-CTCF-ENCFF071FSR-vs-TSS-500bp-outersection1-vs-genes-outersection1
2024-04-29 20:28
1.6M
HEK293-CTCF-ENCFF071FSR-vs-TSS-500bp-outersection1-vs-genes.profiles.files
2024-04-29 15:20
25K
HEK293-CTCF-ENCFF071FSR-vs-TSS-500bp-outersection1-vs-genes.profiles.table
2024-04-29 21:50
2.4M
HEK293-CTCF-ENCFF071FSR.RPM.files
2024-04-19 04:36
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HEK293-CTCF-ENCFF071FSR.RPM.table
2024-04-19 04:36
5.2M
HEK293-CTCF-ENCFF071FSR.SK-L024-Biotin_ATAC_BioTn5_600k-5uM_Kethoxal_pulldown.RPM
2024-04-19 03:52
3.8M
HEK293-CTCF-ENCFF071FSR.SK-L027-HEK293T-KAS_ATAC_input-600k_5uM_Kethoxal_input.RPM
2024-04-19 03:53
3.8M
HEK293-CTCF-ENCFF071FSR.SK-L029-HEK293T-KAS_ATAC_enr-600k_5uM_Kethoxal_pulldown.RPM
2024-04-19 03:50
3.8M
HEK293-FIMO-CIS-BP-vs-G4-intersection1
2024-04-20 03:34
137K
HEK293.KAS_ATAC_peaks.200bp_merge_200bp.RPM-vs-TSS-500bp-intersection1.gz
2024-04-18 09:34
341K
HEK293.KAS_ATAC_peaks.200bp_merge_200bp.RPM-vs-TSS-500bp-outersection1
2024-04-18 09:34
2.2M
HEK293.KAS_ATAC_peaks.200bp_merge_200bp.RPM.files
2021-03-05 17:02
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HEK293.KAS_ATAC_peaks.200bp_merge_200bp.RPM.fraction-preliminary-vs-CTCF-intersection1.gz
2024-04-19 03:36
479K
HEK293.KAS_ATAC_peaks.200bp_merge_200bp.RPM.fraction-preliminary-vs-chroHMM-E1-intersection1.gz
2024-03-20 15:30
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HEK293.KAS_ATAC_peaks.200bp_merge_200bp.RPM.fraction-preliminary-vs-chroHMM-E2-intersection1.gz
2024-03-20 15:30
330K
HEK293.KAS_ATAC_peaks.200bp_merge_200bp.RPM.fraction-preliminary-vs-chroHMM-E3-intersection1.gz
2024-03-20 15:30
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HEK293.KAS_ATAC_peaks.200bp_merge_200bp.RPM.fraction-preliminary-vs-chroHMM-E4-intersection1.gz
2024-03-20 15:30
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HEK293.KAS_ATAC_peaks.200bp_merge_200bp.RPM.fraction-preliminary-vs-chroHMM-E5-intersection1.gz
2024-03-20 15:31
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HEK293.KAS_ATAC_peaks.200bp_merge_200bp.RPM.fraction-preliminary-vs-chroHMM-E6-intersection1.gz
2024-03-20 15:31
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HEK293.KAS_ATAC_peaks.200bp_merge_200bp.RPM.fraction-preliminary-vs-chroHMM-E7-intersection1.gz
2024-03-20 15:30
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HEK293.KAS_ATAC_peaks.200bp_merge_200bp.RPM.fraction-preliminary-vs-chroHMM-E8-intersection1.gz
2024-03-20 15:30
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HEK293.KAS_ATAC_peaks.200bp_merge_200bp.RPM.fraction-preliminary-vs-chroHMM-E9-intersection1.gz
2024-03-20 15:30
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HEK293.KAS_ATAC_peaks.200bp_merge_200bp.RPM.fraction-preliminary-vs-chroHMM-E10-intersection1.gz
2024-03-20 15:30
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HEK293.KAS_ATAC_peaks.200bp_merge_200bp.RPM.fraction-preliminary-vs-chroHMM-E11-intersection1.gz
2024-03-20 15:31
217K
HEK293.KAS_ATAC_peaks.200bp_merge_200bp.RPM.fraction-preliminary-vs-chroHMM-E12-intersection1.gz
2024-03-20 15:30
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HEK293.KAS_ATAC_peaks.200bp_merge_200bp.RPM.fraction-preliminary-vs-chroHMM-E13-intersection1.gz
2024-03-20 15:31
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HEK293.KAS_ATAC_peaks.200bp_merge_200bp.RPM.fraction-preliminary-vs-chroHMM-E14-intersection1.gz
2024-03-20 15:30
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HEK293.KAS_ATAC_peaks.200bp_merge_200bp.RPM.fraction-preliminary-vs-chroHMM-E15-intersection1.gz
2024-03-20 15:30
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HEK293.KAS_ATAC_peaks.200bp_merge_200bp.RPM.fraction-preliminary-vs-chroHMM-E16-intersection1.gz
2024-03-20 15:31
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HEK293.KAS_ATAC_peaks.200bp_merge_200bp.RPM.fraction-preliminary-vs-chroHMM-E17-intersection1.gz
2024-03-20 15:32
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HEK293.KAS_ATAC_peaks.200bp_merge_200bp.RPM.fraction-preliminary-vs-chroHMM-E18-intersection1.gz
2024-03-20 15:35
386K
HEK293.KAS_ATAC_peaks.200bp_merge_200bp.RPM.fraction-preliminary.table.bed
2024-03-20 15:29
5.2M
HEK293.KAS_ATAC_peaks.200bp_merge_200bp.RPM.table
2021-03-05 17:05
3.5M
HEK293.KAS_ATAC_peaks.200bp_merge_200bp.RPM.table.bed
2024-04-18 09:23
3.5M
HEK293.KAS_ATAC_peaks.200bp_merge_200bp.SK-L013-HEK293T-ATAC_100k_cells_5uM_Kethoxal_noPBS_wash_with_biotin_enriched-1.RPM
2021-03-05 17:05
1.6M
HEK293.KAS_ATAC_peaks.200bp_merge_200bp.SK-L013-HEK293T-ATAC_100k_cells_5uM_Kethoxal_noPBS_wash_with_biotin_enriched-1.counts
2021-03-05 17:05
1.3M
HEK293.KAS_ATAC_peaks.200bp_merge_200bp.SK-L014-HEK293T-ATAC_100k_cells_5uM_Kethoxal_noPBS_wash_with_biotin_enriched-2.RPM
2021-03-05 17:05
1.6M
HEK293.KAS_ATAC_peaks.200bp_merge_200bp.SK-L014-HEK293T-ATAC_100k_cells_5uM_Kethoxal_noPBS_wash_with_biotin_enriched-2.counts
2021-03-05 17:05
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HEK293.KAS_ATAC_peaks.200bp_merge_200bp.SK-L017-HEK293T-ATAC_100k_cells_5uM_Kethoxal_noPBS_wash_input-1.RPM
2021-03-05 17:04
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HEK293.KAS_ATAC_peaks.200bp_merge_200bp.SK-L017-HEK293T-ATAC_100k_cells_5uM_Kethoxal_noPBS_wash_input-1.counts
2021-03-05 17:04
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HEK293.KAS_ATAC_peaks.200bp_merge_200bp.SK-L018-HEK293T-ATAC_100k_cells_5uM_Kethoxal_noPBS_wash_input-2.RPM
2021-03-05 17:04
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HEK293.KAS_ATAC_peaks.200bp_merge_200bp.SK-L018-HEK293T-ATAC_100k_cells_5uM_Kethoxal_noPBS_wash_input-2.counts
2021-03-05 17:04
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HEK293.KAS_ATAC_peaks.200bp_merge_200bp.SK-L024-Biotin_ATAC_BioTn5_600k-5uM_Kethoxal_pulldown.RPM
2024-04-19 11:47
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HEK293.KAS_ATAC_peaks.200bp_merge_200bp.SK-L029-HEK293T-KAS_ATAC_enr-600k_5uM_Kethoxal_pulldown.RPM
2024-04-19 11:46
2.0M
HEK293.KAS_ATAC_peaks.200bp_merge_200bp.counts.ATAC-vs-KAS-ATAC-vs-chroHMM
2021-03-06 02:17
27M
HEK293.KAS_ATAC_peaks.200bp_merge_200bp.counts.ATAC-vs-KAS-ATAC-vs-chroHMM-intersection2.hist
2024-03-20 12:03
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HEK293.KAS_ATAC_peaks.200bp_merge_200bp.counts.ATAC-vs-KAS-ATAC.p-adj-0.05-down-vs-chroHMM
2021-03-06 02:30
22M
HEK293.KAS_ATAC_peaks.200bp_merge_200bp.counts.ATAC-vs-KAS-ATAC.p-adj-0.05-down-vs-chroHMM-intersection2.hist
2024-03-20 12:03
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HEK293.KAS_ATAC_peaks.200bp_merge_200bp.counts.ATAC-vs-KAS-ATAC.p-adj-0.05-up-vs-chroHMM
2021-03-06 02:39
23M
HEK293.KAS_ATAC_peaks.200bp_merge_200bp.counts.ATAC-vs-KAS-ATAC.p-adj-0.05-up-vs-chroHMM-intersection2.hist
2024-03-20 12:03
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HEK293.KAS_ATAC_peaks.200bp_merge_200bp.counts.files
2021-03-05 17:02
776
HEK293.KAS_ATAC_peaks.200bp_merge_200bp.counts.table
2021-03-05 17:05
1.9M
HEK293.KAS_ATAC_peaks.200bp_merge_200bp.for_fracton_final_RPM.files
2024-04-19 11:46
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HEK293.KAS_ATAC_peaks.200bp_merge_200bp.for_fracton_final_RPM.table
2024-04-19 11:47
2.2M
HEK293.KAS_ATAC_peaks.200bp_merge_200bp.for_fracton_final_RPM.with_fractions-vs-chroHMM-E1-intersection1.gz
2024-04-19 11:54
457K
HEK293.KAS_ATAC_peaks.200bp_merge_200bp.for_fracton_final_RPM.with_fractions-vs-chroHMM-E2-intersection1.gz
2024-04-19 11:56
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HEK293.KAS_ATAC_peaks.200bp_merge_200bp.for_fracton_final_RPM.with_fractions-vs-chroHMM-E3-intersection1.gz
2024-04-19 11:56
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HEK293.KAS_ATAC_peaks.200bp_merge_200bp.for_fracton_final_RPM.with_fractions-vs-chroHMM-E4-intersection1.gz
2024-04-19 11:56
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HEK293.KAS_ATAC_peaks.200bp_merge_200bp.for_fracton_final_RPM.with_fractions-vs-chroHMM-E5-intersection1.gz
2024-04-19 11:56
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2024-04-19 11:56
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2024-04-19 11:56
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2024-04-19 11:56
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2024-04-19 11:57
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2024-04-19 11:56
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chromBPNet-bias.sh
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chromBPNet-bias_chrombpnet.bigWig
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chromHMM_states.table
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insertLenDist.GM12878_18_segments.files
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