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README.md
README.md
 
 
apa.sh
apa.sh
 
 
apa_kr.sh
apa_kr.sh
 
 
apa_replicate.sh
apa_replicate.sh
 
 
apa_score.sh
apa_score.sh
 
 
bcc_score.py
bcc_score.py
 
 
chromosight.sh
chromosight.sh
 
 
chromosomeloops.xlsx
chromosomeloops.xlsx
 
 
cloops.sh
cloops.sh
 
 
cloops2.sh
cloops2.sh
 
 
clustermap.ipynb
clustermap.ipynb
 
 
convertToBED.sh
convertToBED.sh
 
 
coolpup.sh
coolpup.sh
 
 
counts (2).ipynb
counts (2).ipynb
 
 
ctcf.sh
ctcf.sh
 
 
ctcf_recovery_kr (1).ipynb
ctcf_recovery_kr (1).ipynb
 
 
ctcf_recovery_kr.sh
ctcf_recovery_kr.sh
 
 
ctcf_recovery_raw (1).ipynb
ctcf_recovery_raw (1).ipynb
 
 
ctcf_recovery_raw.sh
ctcf_recovery_raw.sh
 
 
ctcf_recovery_replicate (1).ipynb
ctcf_recovery_replicate (1).ipynb
 
 
ctcf_recovery_replicate.sh
ctcf_recovery_replicate.sh
 
 
deeploop.sh
deeploop.sh
 
 
firecaller.sh
firecaller.sh
 
 
fithic.sh
fithic.sh
 
 
fithichip.sh
fithichip.sh
 
 
h3k27ac_recovery_kr (1).ipynb
h3k27ac_recovery_kr (1).ipynb
 
 
h3k27ac_recovery_kr (2).ipynb
h3k27ac_recovery_kr (2).ipynb
 
 
h3k27ac_recovery_kr.sh
h3k27ac_recovery_kr.sh
 
 
h3k27ac_recovery_raw (1).ipynb
h3k27ac_recovery_raw (1).ipynb
 
 
h3k27ac_recovery_raw (2).ipynb
h3k27ac_recovery_raw (2).ipynb
 
 
h3k27ac_recovery_raw.sh
h3k27ac_recovery_raw.sh
 
 
h3k27ac_recovery_replicate (1).ipynb
h3k27ac_recovery_replicate (1).ipynb
 
 
h3k27ac_recovery_replicate (2).ipynb
h3k27ac_recovery_replicate (2).ipynb
 
 
h3k27ac_recovery_replicate.sh
h3k27ac_recovery_replicate.sh
 
 
hicact.sh
hicact.sh
 
 
hicdc.sh
hicdc.sh
 
 
hicexplorer.sh
hicexplorer.sh
 
 
lasca.sh
lasca.sh
 
 
lineplots.ipynb
lineplots.ipynb
 
 
mustache.sh
mustache.sh
 
 
neo.sh
neo.sh
 
 
overlap.sh
overlap.sh
 
 
partial_apa.sh
partial_apa.sh
 
 
peakachu.sh
peakachu.sh
 
 
primary.sh
primary.sh
 
 
replicate.sh
replicate.sh
 
 
rnapii_recovery_kr (1).ipynb
rnapii_recovery_kr (1).ipynb
 
 
rnapii_recovery_kr.sh
rnapii_recovery_kr.sh
 
 
rnapii_recovery_raw (1).ipynb
rnapii_recovery_raw (1).ipynb
 
 
rnapii_recovery_raw.sh
rnapii_recovery_raw.sh
 
 
rnapii_recovery_replicate (1).ipynb
rnapii_recovery_replicate (1).ipynb
 
 
rnapii_recovery_replicate.sh
rnapii_recovery_replicate.sh
 
 
running_time (2).ipynb
running_time (2).ipynb
 
 
sip.sh
sip.sh
 
 

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Comprehensive_Loop-Caller_Benchmark

BCC Score

bcc_score.py to calculate the BCC Score This script is includes the main formula to calculate the BCC Score with the corresponding categorical scores. This also includes MinMax normalization and scaling formula used in our manuscript.

Results

chromosomeloops.xlsx includes all the raw results from our analysis

Tools Script

.sh scripts includes one shot running commands for every individual tools

Plot Script

.ipynb scripts includes all the python code used for figure generation in our manuscript.

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