Ecosyste.ms: Issues

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GitHub / XiaoTaoWang/NeoLoopFinder issues and pull requests

#70 - How can I use another human reference?

Issue - State: open - Opened by sdjin87 16 days ago

#69 - ‘module 'numpy' has no attribute 'typeDict'’ while searchSVbyGene

Issue - State: open - Opened by Wong718 5 months ago - 2 comments

#68 - Error occurred when Plotting Genes

Issue - State: open - Opened by ZJU-Plumber 6 months ago

#67 - Can neoloopfinder applied to mitosis cells?

Issue - State: open - Opened by Xieeeee 7 months ago - 1 comment

#66 - Pickle has an incompatible dtype

Issue - State: closed - Opened by AudreyBaguette 9 months ago - 1 comment

#65 - segment-cnv and plot-cnv issue

Issue - State: open - Opened by BERICP01 9 months ago

#64 - genome

Issue - State: open - Opened by wangzhaohui-001 9 months ago - 1 comment

#63 - ploidy parameters and biological replicates choose for Down Syndrome

Issue - State: closed - Opened by linfanxiao 11 months ago - 2 comments

#62 - The KeyError: 'weight'

Issue - State: open - Opened by biosciences 12 months ago - 1 comment

#61 - Getting a bug while running vis.plot_genes()

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

#60 - problems in pyensembl_download_cache

Issue - State: closed - Opened by ecesukilinc about 1 year ago

#59 - genes overlapping in visualization

Issue - State: open - Opened by ninashenker over 1 year ago - 2 comments

#58 - the removal of background signals in the plot?

Issue - State: open - Opened by xunchen85 over 1 year ago

#57 - neoloop-caller running error

Issue - State: closed - Opened by xunchen85 over 1 year ago - 1 comment

#56 - what 's the version of pomegranate?

Issue - State: open - Opened by HanwenZhu98 over 1 year ago - 5 comments

#55 - segment-cnv error

Issue - State: open - Opened by abhijitcbio over 1 year ago - 2 comments

#54 - How to plot region not in assembly

Issue - State: open - Opened by Josephinedh over 1 year ago - 2 comments

#53 - Labels overlap with filter

Issue - State: open - Opened by iagooteroc over 1 year ago

#52 - Can I use NeoLoopFinder for other organisms?

Issue - State: open - Opened by xinghua1001 over 1 year ago - 1 comment

#51 - juicer v2 .hic file as the input?

Issue - State: closed - Opened by xunchen85 over 1 year ago - 1 comment

#50 - Log2 Copy Number

Issue - State: closed - Opened by Xieeeee over 1 year ago - 2 comments

#49 - Missed assembled translocations in smaller bins

Issue - State: closed - Opened by xunchen85 almost 2 years ago - 3 comments

#48 - Can we use it with a customized reference genome

Issue - State: closed - Opened by xunchen85 almost 2 years ago - 4 comments

#47 - segment-cnv terminated without notice and results.

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

#46 - NeoLoopFinder for Micro-C

Issue - State: open - Opened by PinpinSui almost 2 years ago - 4 comments

#45 - Numpy.int AttributeError

Issue - State: open - Opened by TeoSakel almost 2 years ago - 1 comment

#44 - Python version in installation commands

Issue - State: closed - Opened by kuba11 almost 2 years ago - 2 comments

#43 - neoloop-caller IndexError

Issue - State: closed - Opened by zzhoujialu almost 2 years ago - 6 comments

#42 - Invalid interval bounds with chr prefix already

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

#41 - Number of Redundant Candidates in assemble-complexSVs

Issue - State: closed - Opened by alobo4 about 2 years ago - 4 comments

#40 - neoloop-caller error

Issue - State: closed - Opened by ldyyzhangh about 2 years ago - 2 comments

#39 - Color of interaction matrix

Issue - State: open - Opened by stanleyrc over 2 years ago - 2 comments
Labels: good first issue

#38 - generating figure has error

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

#37 - The output of neoloop-caller is empty

Issue - State: closed - Opened by yangfeizZZ over 2 years ago

#36 - neoloop-caller failed

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

#35 - neoloop-caller has some error

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

#34 - download pre-trained Peakachu models

Issue - State: open - Opened by Bo-UT over 2 years ago - 8 comments

#33 - visualization of CNV normalization in higlass

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

#32 - Triangle fails to plot some off-diagonal contacts

Issue - State: open - Opened by auberginekenobi almost 3 years ago - 3 comments
Labels: good first issue

#31 - Neoloopfinder doesn't find loops and assemblies that I think it should

Issue - State: open - Opened by auberginekenobi almost 3 years ago - 1 comment
Labels: enhancement

#30 - assemble-complexSVs "Called 0 connected assemblies"

Issue - State: open - Opened by DittmanC about 3 years ago - 1 comment
Labels: enhancement, good first issue

#29 - Run segment-cnv with KeyError: 0

Issue - State: closed - Opened by Yuannyu about 3 years ago - 6 comments

#28 - compatibility with hiChIP data

Issue - State: open - Opened by SplitInf about 3 years ago - 3 comments
Labels: enhancement

#27 - calculate-cnv runtime error

Issue - State: open - Opened by katreya42 about 3 years ago - 4 comments
Labels: bug

#26 - CNV adjustment

Issue - State: open - Opened by DittmanC over 3 years ago - 2 comments
Labels: enhancement

#25 - UnboundLocalError: local variable 'pool' referenced before assignment

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

#24 - Custom enzyme list

Issue - State: closed - Opened by mt96stanley over 3 years ago - 3 comments

#23 - How do I handle cool files

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

#22 - How to output the Regular loop and Tads without SVs

Issue - State: open - Opened by wzhang42 over 3 years ago - 4 comments

#21 - result in error running assemble-complexSVs

Issue - State: open - Opened by zhangli271828 over 3 years ago

#20 - Generating the genome wide loops

Issue - State: open - Opened by wt2855918 over 3 years ago

#19 - input with mouse cells

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

#18 - Some questions for positive and negative training dataset

Issue - State: open - Opened by wzhang42 over 3 years ago - 1 comment

#17 - The discrepancies of neoloop results and neotad results

Issue - State: closed - Opened by wzhang42 over 3 years ago - 2 comments

#15 - problem in converting hic to cool inorder to run neoloop

Issue - State: closed - Opened by zhangli271828 over 3 years ago - 8 comments

#14 - neo-loops/neotad result with the last column as 0 and 1

Issue - State: closed - Opened by wzhang42 over 3 years ago - 6 comments

#13 - missing file K562-test-SVs.txt in tutorial

Issue - State: open - Opened by zhangli271828 over 3 years ago - 3 comments

#12 - What is the strength of the neoloops?

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

#11 - Bugfix for `AttributeError: module 'cooler.ice' has no attribute 'Cooler'`

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

#10 - A# and C# in Assemblies.txt

Issue - State: closed - Opened by wzhang42 over 3 years ago - 3 comments

#9 - Data resource files not downloading correctly

Issue - State: closed - Opened by jrhawley over 3 years ago - 1 comment

#8 - Fail on correct-cnv

Issue - State: closed - Opened by wzhang42 over 3 years ago - 2 comments

#7 - cnv-calculate Runtime Error

Issue - State: closed - Opened by wzhang42 over 3 years ago - 2 comments

#6 - Fail on correct-cnv: issue with cooler.balance

Issue - State: closed - Opened by kokonech over 3 years ago - 10 comments

#4 - What's the best way to generate the simple SV file?

Issue - State: closed - Opened by csijcs over 3 years ago - 7 comments

#3 - CNV segmentation crash

Issue - State: open - Opened by cmdoret over 3 years ago - 11 comments

#2 - AttributeError: module 'rpy2.robjects.numpy2ri' has no attribute 'numpy2ri'

Issue - State: open - Opened by YuanlongLiu over 3 years ago - 4 comments

#1 - calculate-cnv: Invalid interval bounds!

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