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vaquerizaslab
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chess
Comparison of Hi-C Experiments using Structural Similarity.
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Deprecated parameters in scikit-image & scikit-learn
#63
niederhuth
opened
11 months ago
0
Normalization of .hic files
#62
aminakur
opened
1 year ago
1
Chess sim output .tsv file explained
#61
aminakur
opened
1 year ago
1
specify data_range in structural_similarity call
#60
nickmachnik
closed
1 year ago
0
data_range parameter not specified - error
#59
aminakur
closed
1 year ago
7
chess extract error: operands could not be broadcast together with shapes
#58
zy041225
closed
7 months ago
1
_pickle.PicklingError
#57
PengfeiInTuebingen
opened
2 years ago
2
something different from plotting
#56
ZQY19960810
closed
2 years ago
9
error when running extract on .hic files
#55
ZQY19960810
opened
2 years ago
1
error on running chess sim
#54
ZQY19960810
closed
2 years ago
2
issue of normalized/chess extract
#53
ZQY19960810
closed
2 years ago
1
error of the chess extract
#52
ZQY19960810
closed
2 years ago
3
speed up the chess run
#51
zy041225
closed
2 years ago
1
conservation analysis when only a few syntenic blocks are available
#50
zy041225
closed
3 years ago
3
Should the users be concerned about the problem raised in the new Contradictory Results bioRxiv preprint?
#49
P-GB-W
opened
3 years ago
2
Different resolution produce different result
#48
biozzq
opened
3 years ago
1
No valid region pairs found?
#47
gdolsten
opened
3 years ago
1
Nan Continued
#46
drlaurenwasson
closed
3 years ago
2
Conditions for conservation analysis of syntenic blocks
#45
luciaalvarez95
opened
3 years ago
5
CNV bias in normalization
#44
jazberna1
closed
3 years ago
2
Add coordinate conversion helpers
#43
cmdoret
closed
3 years ago
5
"chess --version" now works correctly
#42
liz-is
closed
3 years ago
1
chess --version doesn't work?
#41
liz-is
closed
3 years ago
0
Updated FAQ and added BEDPE format explanations
#40
liz-is
closed
3 years ago
1
Get observed/expected from Juicer Hi-C
#39
sshen82
closed
3 years ago
2
Error when running CHESS on JUICER HIC files
#38
rkuzya
opened
3 years ago
2
BEDPE file format
#37
ysora
closed
3 years ago
3
No valid pairs found problem
#36
sshen82
closed
3 years ago
5
Prepare the normalized hic input for CHESS
#35
biozzq
opened
3 years ago
9
It's difficult to find any significant changes in 3D organization of chromatin in highly dissimilar regions
#34
biozzq
opened
3 years ago
14
Modified pairs creation so BEDPE is 0-based
#33
liz-is
closed
3 years ago
1
BED / BEDPE file handling - BEDPE file produced by `chess pairs` is not 0-based
#32
liz-is
closed
3 years ago
3
how to deal with biological replicate
#31
biozzq
closed
3 years ago
4
Could not compute similarity for...
#30
liz-is
closed
3 years ago
4
how to get the actual positions of the highly dissimilar regions highlighted by chess extract
#29
biozzq
closed
3 years ago
4
questions about the results of chess extract
#28
biozzq
closed
3 years ago
8
chess filter Unrecognized command
#27
biozzq
closed
3 years ago
2
How to define the high confidence set of regions showing clear changes?
#26
biozzq
closed
3 years ago
2
Error when run chess_extract
#25
yanchunzhang
opened
3 years ago
3
plot output?
#24
rikrdo89
opened
3 years ago
1
Chess sim quits with ERROR "all regions need to span at least 20 bins "
#23
rikrdo89
opened
4 years ago
16
non
#22
BenxiaHu
closed
4 years ago
0
The example hic file cannot be dumped
#21
biozzq
closed
3 years ago
4
Run time of chess sim module
#20
magnitov
closed
4 years ago
7
Error while running "example analysis"
#19
Gonysh
closed
4 years ago
2
Chess sim command runtime improvement heuristics?
#18
jmcbroome
opened
4 years ago
6
non
#17
BenxiaHu
closed
4 years ago
1
chess sim result wit all NAN
#16
chenggang108
opened
4 years ago
13
non
#15
BenxiaHu
closed
4 years ago
1
non
#14
BenxiaHu
closed
4 years ago
2
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