elsasserlab/GLOE-analysis-published.zip
elsasserlab-GLOE-analysis-77db5a9
.DS_Store
12.3 kB
.gitattributes
66 Bytes
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README.md
18 Bytes
analysis
.DS_Store
6.1 kB
.Rhistory
6.2 kB
210121 Gloe-seq.R
4.1 kB
210126 Gloe-seq.R
4.7 kB
CAD-ctrl.pdf
11.0 kB
CAD-peaks.pdf
11.0 kB
CAD-peaks.rep.pdf
11.0 kB
GLOE-CTCF.Rmd
6.7 kB
GLOE-CTCF.nb.html
4.1 MB
GLOE-ChromHMM.Rmd
1.8 kB
GLOE-ChromHMM.nb.html
1.5 MB
GLOE-atac.Rmd
1.5 kB
GLOE-atac.nb.html
676.4 kB
GLOE-frac_under_pileup.Rmd
1.2 kB
GLOE-frac_under_pileup.nb.html
926.3 kB
GLOE-pileups.Rmd
8.4 kB
GLOE-pileups.backup.html
4.6 MB
GLOE-pileups.nb.html
3.1 MB
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chromhmm.pdf
8.2 kB
chromhmm.txt
4.3 kB
frac_under_pile.pdf
6.1 kB
pileup-atac-heatmap.pdf
347.5 kB
pileup-atac-profile.pdf
8.3 kB
pileup-heatmap.pdf
20.9 kB
pileup-peaks.pdf
21.8 kB
profile-ctcf-atac-dhs.pdf
24.4 kB
profile-ctcf-pos.pdf
20.1 kB
profile-dhs-pos.pdf
20.5 kB
stats_piles.pdf
77.6 kB
data
.DS_Store
8.2 kB
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pileup-WT-24hr
GL-WT-24hr-3.pile_up3_s10_u.bed
2.0 kB
GL-WT-24hr-3.pile_up3_s10_u.shuffled.ChromHMM_annotation.bed
2.0 kB
GL-WT-24hr-3.pile_up3_s10_u.shuffled.ChromHMM_annotation.txt
48 Bytes
GL-WT-24hr-3.pile_up3_s10_u.shuffled.bed
960 Bytes
GL-WT-24hr-3.pile_up3_s10_u.uniq.CTCF_annotation.bed
880 Bytes
GL-WT-24hr-3.pile_up3_s10_u.uniq.ChromHMM_annotation.bed
2.0 kB
GL-WT-24hr-3.pile_up3_s10_u.uniq.ChromHMM_annotation.txt
57 Bytes
GL-WT-24hr-3.pile_up3_s10_u.uniq.bed
954 Bytes
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macs2_results.pile_up3_s10_u.txt
280 Bytes
pileup1.svg
21.2 kB
pileup2.svg
186.5 kB
run.pile_up3_s10_u.sbatch
6.5 kB
pileup-analysis
.DS_Store
6.1 kB
GL-WT-24hr-3.copeaks.uniq.bed
1.1 kB
GL-WT-24hr-3.minus.uniq.bed
16.0 kB
GL-WT-24hr-3.plus.uniq.bed
17.0 kB
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filter_stats.txt
214 Bytes
merge_bam_cov_downsample.sbatch
10.6 kB
motif
GL-KO-20-5.count.txt
5 Bytes
GL-KO-20-5.motif_shift20_counts_pos1-6.txt
19.8 kB
GL-KO-20-5.pileup.motif.range.bed
153.9 kB
GL-KO-20-5.pileup.motif.reads.fasta
166.6 kB
GL-KO-20-5motif_shift20_counts_pos3-5.txt
768 Bytes
GL-KO-20-5motif_shift20_counts_pos3-6.txt
3.1 kB
GL-KO-20-5motif_shift20_counts_pos4-5.txt
176 Bytes
GL-KO-24hr-6.count.txt
5 Bytes
GL-KO-24hr-6.motif_shift20_counts_pos1-6.txt
15.5 kB
GL-KO-24hr-6.pileup.motif.range.bed
133.8 kB
GL-KO-24hr-6.pileup.motif.reads.fasta
144.9 kB
GL-KO-24hr-6motif_shift20_counts_pos3-5.txt
780 Bytes
GL-KO-24hr-6motif_shift20_counts_pos3-6.txt
3.0 kB
GL-KO-24hr-6motif_shift20_counts_pos4-5.txt
187 Bytes
GL-KO-UT-4.count.txt
5 Bytes
GL-KO-UT-4.motif_shift20_counts_pos1-6.txt
25.9 kB
GL-KO-UT-4.pileup.motif.range.bed
240.2 kB
GL-KO-UT-4.pileup.motif.reads.fasta
259.8 kB
GL-KO-UT-4motif_shift20_counts_pos3-5.txt
768 Bytes
GL-KO-UT-4motif_shift20_counts_pos3-6.txt
3.2 kB
GL-KO-UT-4motif_shift20_counts_pos4-5.txt
176 Bytes
GL-WT-20-2.count.txt
5 Bytes
GL-WT-20-2.motif_shift20_counts_pos1-6.txt
25.7 kB
GL-WT-20-2.pileup.motif.range.bed
236.6 kB
GL-WT-20-2.pileup.motif.reads.fasta
255.9 kB
GL-WT-20-2motif_shift20_counts_pos3-5.txt
768 Bytes
GL-WT-20-2motif_shift20_counts_pos3-6.txt
3.2 kB
GL-WT-20-2motif_shift20_counts_pos4-5.txt
176 Bytes
GL-WT-24hr-3.count.txt
5 Bytes
GL-WT-24hr-3.motif_shift20_counts_pos1-6.txt
11.7 kB
GL-WT-24hr-3.pileup.motif.range.bed
363.8 kB
GL-WT-24hr-3.pileup.motif.reads.fasta
393.5 kB
GL-WT-24hr-3motif_shift20_counts_pos3-5.txt
456 Bytes
GL-WT-24hr-3motif_shift20_counts_pos3-6.txt
1.7 kB
GL-WT-24hr-3motif_shift20_counts_pos4-5.txt
116 Bytes
GL-WT-UT-1.count.txt
5 Bytes
GL-WT-UT-1.motif_shift20_counts_pos1-6.txt
24.9 kB
GL-WT-UT-1.pileup.motif.range.bed
220.6 kB
GL-WT-UT-1.pileup.motif.reads.fasta
238.9 kB
GL-WT-UT-1motif_shift20_counts_pos3-5.txt
768 Bytes
GL-WT-UT-1motif_shift20_counts_pos3-6.txt
3.2 kB
GL-WT-UT-1motif_shift20_counts_pos4-5.txt
176 Bytes
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logo-2.pdf
11.5 kB
logo-4.pdf
11.9 kB
logo-6.pdf
12.1 kB
logo.pdf
12.5 kB
motif_kmers.xlsx
14.7 kB
pileup_fractions.txt
485 Bytes
pileup_stats.txt
424 Bytes
qc
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fingerprint.pdf
384.6 kB
genome
.DS_Store
6.1 kB
10kb.hg19.chr10.bed
349.1 kB
1kb.hg19.chr10.bed
3.5 MB
5kb.hg19.chr10.bed
698.1 kB
HCT116_ATACseq.hg19.bed
2.6 MB
HCT116_CTCF.hg19.bed
2.4 MB
HCT116_DHS.hg19.bed
2.8 MB
HCT116_KAP1.hg19.bed
985.3 kB
HCT116_MYC.hg19.bed
2.0 MB
HCT116_RNAP2.hg19.bed
803.0 kB
HCT116_TOPI.hg19.bed
295.0 kB
HCT116_YY1.hg19.bed
1.9 MB
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RefGene_uniqueTSS.lt10kb.hg19.bed
703.5 kB
Thompson2018_HCT116_WT_ChromHMM10.bed
12.8 MB
Thompson2018_HCT116_WT_ChromHMM10.chr22.bed
258.9 kB
Thompson2018_HCT116_WT_ChromHMM10.chr3.bed
810.4 kB
consensusBlacklist.hg19.bed
18.8 kB
hg19.chrom.sizes
365 Bytes
repmasker.bed
1.0 MB
lib
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lib_embed_data.v1.0.R
736 Bytes
lib_trackplot.v1.0.R
53.1 kB
scripts
.DS_Store
6.1 kB
simple_pipeline_PE_hg19_mm9.sbatch
3.5 kB
simple_pipeline_wrapper_PE_hg19_v2.sh
195 Bytes