Ecosyste.ms: Issues

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GitHub / vaquerizaslab/chess issues and pull requests

#63 - Deprecated parameters in scikit-image & scikit-learn

Issue - State: open - Opened by niederhuth 10 months ago

#62 - Normalization of .hic files

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

#61 - Chess sim output .tsv file explained

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

#60 - specify data_range in structural_similarity call

Pull Request - State: closed - Opened by nickmachnik about 1 year ago

#59 - data_range parameter not specified - error

Issue - State: closed - Opened by MyBiscuit about 1 year ago - 7 comments
Labels: bug

#58 - chess extract error: operands could not be broadcast together with shapes

Issue - State: closed - Opened by zy041225 about 2 years ago - 1 comment

#57 - _pickle.PicklingError

Issue - State: open - Opened by PengfeiInTuebingen about 2 years ago - 2 comments

#56 - something different from plotting

Issue - State: closed - Opened by ZQY19960810 over 2 years ago - 9 comments

#55 - error when running extract on .hic files

Issue - State: open - Opened by ZQY19960810 over 2 years ago - 1 comment

#54 - error on running chess sim

Issue - State: closed - Opened by ZQY19960810 over 2 years ago - 2 comments

#53 - issue of normalized/chess extract

Issue - State: closed - Opened by ZQY19960810 over 2 years ago - 1 comment

#52 - error of the chess extract

Issue - State: closed - Opened by ZQY19960810 almost 3 years ago - 3 comments

#51 - speed up the chess run

Issue - State: closed - Opened by zy041225 almost 3 years ago - 1 comment

#50 - conservation analysis when only a few syntenic blocks are available

Issue - State: closed - Opened by zy041225 almost 3 years ago - 3 comments

#48 - Different resolution produce different result

Issue - State: open - Opened by biozzq about 3 years ago - 1 comment

#47 - No valid region pairs found?

Issue - State: open - Opened by gdolsten over 3 years ago - 1 comment

#46 - Nan Continued

Issue - State: closed - Opened by drlaurenwasson over 3 years ago - 2 comments

#45 - Conditions for conservation analysis of syntenic blocks

Issue - State: open - Opened by luciaalvarez95 over 3 years ago - 5 comments

#44 - CNV bias in normalization

Issue - State: closed - Opened by jazberna1 over 3 years ago - 2 comments

#43 - Add coordinate conversion helpers

Pull Request - State: closed - Opened by cmdoret over 3 years ago - 5 comments

#42 - "chess --version" now works correctly

Pull Request - State: closed - Opened by liz-is over 3 years ago - 1 comment

#41 - chess --version doesn't work?

Issue - State: closed - Opened by liz-is over 3 years ago

#40 - Updated FAQ and added BEDPE format explanations

Pull Request - State: closed - Opened by liz-is over 3 years ago - 1 comment

#39 - Get observed/expected from Juicer Hi-C

Issue - State: closed - Opened by sshen82 over 3 years ago - 2 comments

#38 - Error when running CHESS on JUICER HIC files

Issue - State: open - Opened by rkuzya over 3 years ago - 2 comments

#37 - BEDPE file format

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

#36 - No valid pairs found problem

Issue - State: closed - Opened by sshen82 over 3 years ago - 5 comments

#35 - Prepare the normalized hic input for CHESS

Issue - State: open - Opened by biozzq over 3 years ago - 9 comments

#33 - Modified pairs creation so BEDPE is 0-based

Pull Request - State: closed - Opened by liz-is over 3 years ago - 1 comment

#32 - BED / BEDPE file handling - BEDPE file produced by `chess pairs` is not 0-based

Issue - State: closed - Opened by liz-is over 3 years ago - 3 comments

#31 - how to deal with biological replicate

Issue - State: closed - Opened by biozzq over 3 years ago - 4 comments

#30 - Could not compute similarity for...

Issue - State: closed - Opened by liz-is over 3 years ago - 4 comments

#28 - questions about the results of chess extract

Issue - State: closed - Opened by biozzq almost 4 years ago - 8 comments

#27 - chess filter Unrecognized command

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

#26 - How to define the high confidence set of regions showing clear changes?

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

#25 - Error when run chess_extract

Issue - State: open - Opened by yanchunzhang almost 4 years ago - 3 comments

#24 - plot output?

Issue - State: open - Opened by rikrdo89 almost 4 years ago - 1 comment

#23 - Chess sim quits with ERROR "all regions need to span at least 20 bins "

Issue - State: open - Opened by rikrdo89 almost 4 years ago - 16 comments

#22 - non

Issue - State: closed - Opened by BenxiaHu almost 4 years ago

#21 - The example hic file cannot be dumped

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

#20 - Run time of chess sim module

Issue - State: closed - Opened by magnitov almost 4 years ago - 7 comments

#19 - Error while running "example analysis"

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

#18 - Chess sim command runtime improvement heuristics?

Issue - State: open - Opened by jmcbroome almost 4 years ago - 6 comments

#17 - non

Issue - State: closed - Opened by BenxiaHu almost 4 years ago - 1 comment

#16 - chess sim result wit all NAN

Issue - State: open - Opened by chenggang108 almost 4 years ago - 13 comments

#15 - non

Issue - State: closed - Opened by BenxiaHu almost 4 years ago - 1 comment

#14 - non

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

#13 - non

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

#12 - The input image seems to have just one color 0.

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

#11 - hints to chess extract

Issue - State: open - Opened by cgirardot almost 4 years ago - 1 comment

#10 - Extracting genomic coordinates of differential features

Issue - State: open - Opened by cgirardot almost 4 years ago - 17 comments
Labels: enhancement, good first issue

#9 - NaN continued

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

#8 - closed

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

#6 - chess extract fails with `ValueError: Image must contain only positive values`

Issue - State: closed - Opened by cgirardot almost 4 years ago - 19 comments

#5 - chess sim results are all nan

Issue - State: closed - Opened by Irenexzwen almost 4 years ago - 6 comments

#4 - ValueError: range() arg 3 must not be zero

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

#3 - 'Series' object has no attribute 'bias' in `chess sim`

Issue - State: closed - Opened by nickmachnik almost 4 years ago - 17 comments

#2 - non

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

#1 - Error when a chromosome in the pairs file is not in the HiC matrix

Issue - State: closed - Opened by MariaRig over 4 years ago - 1 comment
Labels: enhancement