koszullab/chromosight issues and pull requests

#64 - Recommend parameters of borders detect

Issue - State: open - Opened by yizhang-zoey over 1 year ago - 1 comment

#63 - Pattern = TAD?

Issue - State: open - Opened by MyBiscuit over 1 year ago - 1 comment

#62 - Loop score calculation

Issue - State: open - Opened by WanyingX almost 2 years ago - 4 comments
Labels: question

#61 - Add CodeQL workflow for GitHub code scanning

Pull Request - State: closed - Opened by lgtm-com[bot] about 2 years ago

#60 - Where do these kernels come from?

Issue - State: closed - Opened by zhyanlin about 2 years ago - 5 comments
Labels: question

#59 - replace deprecated scipy median_absolute_deviation

Pull Request - State: closed - Opened by cmdoret over 2 years ago - 1 comment

#58 - Is there a way to use multiresolution .mcool files directly?

Issue - State: closed - Opened by Elphege-Nora over 2 years ago - 1 comment
Labels: question

#57 - How does Chromosight compute the Pearson correlation ?

Issue - State: open - Opened by GeorgyChistov over 2 years ago - 2 comments
Labels: question

#56 - Bus error in chromosight quantify

Issue - State: closed - Opened by mannekim over 2 years ago - 2 comments

#55 - Can chromosight detect loops based on restriction fragments level (1f, 2f, etc) HI-C matrix.

Issue - State: closed - Opened by Linhua-Sun almost 3 years ago - 2 comments

#54 - chromosight detects hairpin, the numer is too large

Issue - State: open - Opened by HongguiWu1 almost 3 years ago - 1 comment

#53 - Different number of loops on GM12878 Hi-C map

Issue - State: closed - Opened by zhang-jiankun about 3 years ago - 2 comments

#52 - How to evaluate the detected loops?

Issue - State: closed - Opened by frankchen121212 over 3 years ago - 4 comments
Labels: question

#51 - Different number of patterns for the same Hi-C matrix

Issue - State: closed - Opened by magnitov over 3 years ago - 3 comments
Labels: bug

#50 - Point and click mode

Issue - State: closed - Opened by ysora over 3 years ago - 8 comments
Labels: help wanted

#49 - Chromosight for single-cell Hi-C

Issue - State: closed - Opened by HongguiWu1 over 3 years ago - 8 comments

#48 - Questions about resolution in loop json file

Issue - State: closed - Opened by Linhua-Sun over 3 years ago - 2 comments
Labels: question

#47 - How to compare loops of Hi-C from different conditions like DEG in RNA-Seq?

Issue - State: closed - Opened by Linhua-Sun over 3 years ago - 4 comments
Labels: question

#46 - Different score values between chromosight detect and chromosight quantify on borders pattern

Issue - State: closed - Opened by tfoutelrodier over 3 years ago - 2 comments
Labels: bug

#45 - Detection doesn't report loops that should pass the Pearson threshold

Issue - State: closed - Opened by PerrineLacour over 3 years ago - 4 comments
Labels: question

#44 - Chromosight quantification time complexity

Issue - State: closed - Opened by PerrineLacour over 3 years ago - 4 comments
Labels: question

#43 - Use chromosight to quantify chromatin interactions on domain (TAD or local domains)

Issue - State: closed - Opened by Linhua-Sun almost 4 years ago - 5 comments
Labels: question

#42 - Input to simulated data

Issue - State: closed - Opened by gdolsten almost 4 years ago - 4 comments
Labels: help wanted

#41 - TypeError: ufunc 'isnan' not supported for the input types

Issue - State: closed - Opened by jazberna1 almost 4 years ago - 11 comments
Labels: bug

#40 - qvalues are always smaller than the pvalue

Issue - State: closed - Opened by jazberna1 almost 4 years ago - 4 comments

#39 - only one contact matrix gets processed

Issue - State: closed - Opened by jazberna1 almost 4 years ago - 3 comments

#38 - run chromosight with --inter option on each interchromosome matrix separately

Issue - State: closed - Opened by jazberna1 almost 4 years ago - 2 comments

#37 - Scaling of kernel

Issue - State: closed - Opened by PerrineLacour almost 4 years ago - 2 comments
Labels: question

#36 - call peaks between different chromosomes

Issue - State: closed - Opened by jazberna1 almost 4 years ago - 3 comments
Labels: question

#35 - Empty score fields in quantify results

Issue - State: closed - Opened by PerrineLacour almost 4 years ago - 4 comments

#34 - Plotting

Issue - State: closed - Opened by sarah872 about 4 years ago - 2 comments
Labels: question

#33 - Raw or Norm counts cool

Issue - State: closed - Opened by cgirardot about 4 years ago - 4 comments
Labels: question

#32 - Rect speedup

Pull Request - State: closed - Opened by cmdoret about 4 years ago - 1 comment

#31 - Switch to MIT license

Pull Request - State: closed - Opened by cmdoret about 4 years ago

#30 - Cli norm

Pull Request - State: closed - Opened by cmdoret about 4 years ago - 1 comment

#29 - List kernels

Pull Request - State: closed - Opened by cmdoret about 4 years ago - 2 comments

#28 - Prefix

Pull Request - State: closed - Opened by cmdoret over 4 years ago - 2 comments

#27 - output file name

Issue - State: closed - Opened by Phlya over 4 years ago - 8 comments

#26 - Correlation score

Issue - State: closed - Opened by jessakay over 4 years ago - 2 comments
Labels: help wanted

#25 - Full as default

Pull Request - State: closed - Opened by cmdoret over 4 years ago - 1 comment

#24 - Reported coordinates seem shifted

Issue - State: closed - Opened by Phlya over 4 years ago - 2 comments

#23 - Pvalue

Pull Request - State: closed - Opened by cmdoret over 4 years ago

#22 - tSVD

Pull Request - State: closed - Opened by cmdoret over 4 years ago - 1 comment

#21 - Memory optimisation

Pull Request - State: closed - Opened by cmdoret over 4 years ago - 2 comments

#20 - replace precision threshold by an absolute threshold

Pull Request - State: closed - Opened by cmdoret over 4 years ago

#19 - Partial convolution

Pull Request - State: closed - Opened by cmdoret almost 5 years ago

#18 - Testing command and file-like object support

Pull Request - State: closed - Opened by cmdoret almost 5 years ago - 1 comment

#17 - Dev

Pull Request - State: closed - Opened by cmdoret almost 5 years ago - 1 comment

#16 - Four way adj

Pull Request - State: closed - Opened by cmdoret almost 5 years ago - 1 comment

#15 - Optimise memory usage

Issue - State: closed - Opened by cmdoret almost 5 years ago
Labels: enhancement

#14 - Tests

Pull Request - State: closed - Opened by cmdoret about 5 years ago

#13 - Dev

Pull Request - State: closed - Opened by cmdoret about 5 years ago

#12 - Tests

Pull Request - State: closed - Opened by cmdoret about 5 years ago

#11 - Tests

Pull Request - State: closed - Opened by cmdoret about 5 years ago

#10 - Dev

Pull Request - State: closed - Opened by cmdoret about 5 years ago - 1 comment

#9 - additional features

Issue - State: closed - Opened by cmdoret about 5 years ago
Labels: enhancement

#8 - Dev

Pull Request - State: closed - Opened by cmdoret about 5 years ago - 1 comment

#7 - Proper packaging

Issue - State: closed - Opened by cmdoret about 5 years ago
Labels: documentation

#6 - Dev

Pull Request - State: closed - Opened by cmdoret about 5 years ago

#5 - simplify objects

Issue - State: closed - Opened by cmdoret about 5 years ago - 1 comment

#4 - Refactor

Pull Request - State: closed - Opened by cmdoret about 5 years ago

#3 - Adding of quantification of pattern

Issue - State: closed - Opened by axelcournac over 5 years ago - 1 comment

#2 - Features to add and things to improve

Issue - State: closed - Opened by cmdoret over 5 years ago - 8 comments
Labels: enhancement

#1 - Remove bottleneck "np.where" in utils.picker

Issue - State: closed - Opened by cmdoret over 5 years ago - 1 comment
Labels: enhancement

GitHub / koszullab/chromosight issues and pull requests