koszullab chromosight issues

koszullab / chromosight

Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps

https://chromosight.readthedocs.io

Other

63 stars 9 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

plots appear blurry

#68 ratheraarif opened 4 months ago
0
Handle variable bin size

#67 cmdoret opened 1 year ago
0
HicMatrix generated cool file not supported - possible solution

#66 Mestizia closed 1 year ago
6
Tuning the parameters (perc-zero, perc-undetected, pearson) for a relatively small dataset

#65 ZianFang opened 1 year ago
2
Recommend parameters of borders detect

#64 yizhang-zoey opened 1 year ago
1
Pattern = TAD?

#63 aminakur closed 1 year ago
1
Loop score calculation

#62 WanyingX closed 1 year ago
4
Add CodeQL workflow for GitHub code scanning

#61 lgtm-com[bot] closed 2 years ago
0
Where do these kernels come from?

#60 zhyanlin closed 2 years ago
5
replace deprecated scipy median_absolute_deviation

#59 cmdoret closed 2 years ago
1
Is there a way to use multiresolution .mcool files directly?

#58 Elphege-Nora closed 1 year ago
1
How does Chromosight compute the Pearson correlation ?

#57 GeorgyChistov closed 1 year ago
2
Bus error in chromosight quantify

#56 mannekim closed 1 year ago
2
Can chromosight detect loops based on restriction fragments level (1f, 2f, etc) HI-C matrix.

#55 Linhua-Sun closed 2 years ago
2
chromosight detects hairpin, the numer is too large

#54 HongguiWu1 closed 1 year ago
1
Different number of loops on GM12878 Hi-C map

#53 zhang-jiankun closed 3 years ago
2
How to evaluate the detected loops?

#52 frankchen121212 closed 3 years ago
4
Different number of patterns for the same Hi-C matrix

#51 magnitov closed 3 years ago
3
Point and click mode

#50 ysora closed 3 years ago
8
Chromosight for single-cell Hi-C

#49 HongguiWu1 closed 3 years ago
8
Questions about resolution in loop json file

#48 Linhua-Sun closed 3 years ago
2
How to compare loops of Hi-C from different conditions like DEG in RNA-Seq?

#47 Linhua-Sun closed 3 years ago
4
Different score values between chromosight detect and chromosight quantify on borders pattern

#46 tfoutelrodier closed 3 years ago
2
Detection doesn't report loops that should pass the Pearson threshold

#45 PerrineLacour closed 3 years ago
4
Chromosight quantification time complexity

#44 PerrineLacour closed 3 years ago
4
Use chromosight to quantify chromatin interactions on domain (TAD or local domains)

#43 Linhua-Sun closed 3 years ago
5
Input to simulated data

#42 gdolsten closed 3 years ago
4
TypeError: ufunc 'isnan' not supported for the input types

#41 jazberna1 closed 3 years ago
11
qvalues are always smaller than the pvalue

#40 jazberna1 closed 3 years ago
4
only one contact matrix gets processed

#39 jazberna1 closed 3 years ago
3
run chromosight with --inter option on each interchromosome matrix separately

#38 jazberna1 closed 3 years ago
2
Scaling of kernel

#37 PerrineLacour closed 3 years ago
2
call peaks between different chromosomes

#36 jazberna1 closed 3 years ago
3
Empty score fields in quantify results

#35 PerrineLacour closed 3 years ago
4
Plotting

#34 sarah872 closed 4 years ago
2
Raw or Norm counts cool

#33 cgirardot closed 4 years ago
4
Rect speedup

#32 cmdoret closed 4 years ago
1
Switch to MIT license

#31 cmdoret closed 4 years ago
0
Cli norm

#30 cmdoret closed 4 years ago
1
List kernels

#29 cmdoret closed 4 years ago
2
Prefix

#28 cmdoret closed 4 years ago
2
output file name

#27 Phlya closed 4 years ago
8
Correlation score

#26 jessakay closed 4 years ago
2
Full as default

#25 cmdoret closed 4 years ago
1
Reported coordinates seem shifted

#24 Phlya closed 4 years ago
2
Pvalue

#23 cmdoret closed 4 years ago
0
tSVD

#22 cmdoret closed 4 years ago
1
Memory optimisation

#21 cmdoret closed 4 years ago
2
replace precision threshold by an absolute threshold

#20 cmdoret closed 4 years ago
0
Partial convolution

#19 cmdoret closed 4 years ago
0