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Joachim Wolff joachimwolff Friedrich Miescher Institute for Biomedical Research Basel, Switzerland

deeptools/pyGenomeTracks 525

python module to plot beautiful and highly customizable genome browser tracks

galaxyproject/training-material 217

A collection of Galaxy-related training material

deeptools/HiCExplorer 143

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.

bgruening/rbc_docs 4

RBC de.NBI documents

joachimwolff/algorithmsInBioinformatics 4

Bioinformatics algorithms: Needleman-Wunsch, Feng-Doolittle, Gotoh and Nussinov implemented in Python

deeptools/hicBuildMatrixCpp 2

C++ implementation of hicBuildMatrix

joachimwolff/galaxyhowto 2

First steps to configure a vanilla galaxy instance

joachimwolff/chicago 1

Fork of the CHiCAGO package from Babraham Institute, Cambridge hosted on bitbucket

issue commentdeeptools/HiCExplorer

"HiCMatrix does not exist" error when using hicMergeMatrixBins

HI Amina,

this error is confusing. It says hicMatrix does not exists, but it the rest of the error message indicates that the error comes exactly from this non-existing library. Given the rest of the error message and the check for check_file_access seems to throw the error, I assume it is maybe caused that it cannot access either your input or output file. Can you please check if a) the input file really exists (typos; access to paths; are you in the right folder etc?) and also for the output if the given file path is accessible.

I hope this helps to solve the issue.

Best,

Joachim

husseinao

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issue commentdeeptools/HiCExplorer

HiCBrowser Compatibility

@LeilyR That's something MPI needs to answer.

matanel-y

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issue commentdeeptools/HiCExplorer

Error with hicFindTADs

Hi,

the file ending in command (a) is wrong. First, you write hdf5 instead of h5. However, h5 is our HiCExplorer specific file format, and I don't think a study from 2016 used HiCExplorer to create their files! I know it is a bit confusing, but hdf5 is a generalised container format, we just use it, but the internal structure of the file is specific to HiCExplorer. For (b) you specify a h5 but it tries to load a cool file. And then it complains that certain data structures are not available. This indicates that the file you try to load is neither a HiCExplorer specific h5 nor a cool file.

To confirm my assumption, I downloaded one of the files of the given GSE, and yes, the content looks very different from what we are expecting for HiCExplorer:

Screenshot 2022-01-05 at 11 13 43

Compare to: https://hicexplorer.readthedocs.io/en/latest/content/file-formats.html#interaction-matrix-format-h5

Long story short: Please try to load data formats that HiCExplorer actually supports!

Best,

Joachim

spiderzbh

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issue commentdeeptools/HiCExplorer

How to filter the results from `hicDifferentialTAD` based in p-value and W values?

Hi,

  • have you normalised the data of the two matrices and if, how?
  • can you please provided a plot of a specific region with the TADs as an example?
  • you can also change the p-value that is used to decide acceptance / rejection
  • Have in mind H0 is 'regions are equal' and 'acceptance' means this condition is fulfilled.
  • What is your expectation? Shall there be major differences in the TADs or are the samples more or less equal?

Best,

Joachim

Linhua-Sun

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issue commentdeeptools/HiCExplorer

hicInterIntraTAD: ZeroDivisionError: division by zero

Hi Mikhail,

Thanks for reporting this bug. I will take care to fix it.

Best,

Joachim

mdozmorov

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issue commentdeeptools/HiCExplorer

hicHyperoptDetectLoops

It's a file containing the information where proteins are located, for example ChIP-Seq CTCF data. https://raw.githubusercontent.com/deeptools/HiCExplorer/master/hicexplorer/test/test_data/hicHyperoptDetectLoops/ctcf_sorted.bed However, to just detect loops please use hicDetectLoops. The tool you listed is only for parameter optimisation of hicDetectLoops: https://hicexplorer.readthedocs.io/en/latest/content/tools/hicDetectLoops.html#hicdetectloops

zhanglp996

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issue commentdeeptools/HiCExplorer

hicPCA and compartmentalization. Setting interaction range.

Thanks for your contribution, but I don't get your point. A different input will lead to a different result, that's quite clear. However, even if the result is not 1:1 comparable to a PCA on the full matrix, and also if the result is something else in mathematical terms, it might still be a valid result in terms of biological interpretation. You always need to verify your results with orthogonal data, and if that shows it's valid, the approach can be used. Therefore I am not sure what kind of issue you are raising here.

kimj50

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issue closeddeeptools/HiCExplorer

Installation error

Unable to install using conda conda create --name hicexplorer hicexplorer=3.6 python=3.8 -c bioconda -c conda-forge Collecting package metadata (current_repodata.json): done Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: - Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package python conflicts for: python=3.8 hicexplorer=3.6 -> python[version='>=3.6'] hicexplorer=3.6 -> biopython[version='<1.77'] -> python[version='2.7.|3.5.|3.6.|>=2.7,<2.8.0a0|>=3.7,<3.8.0a0|>=3.8,<3.9.0a0|>=3.6,<3.7.0a0|>=3.5,<3.6.0a0|<3.7|>=3.9,<3.10.0a0|>=3.10,<3.11.0a0|3.4.|>=3|>=3.7.1,<3.8.0a0|>=2.7|>=3.5|2.7|>=3.5']

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blessyantony9

issue commentdeeptools/HiCExplorer

Installation error

We checked it and can recommend mamba in case the conda solver needs too much time. Concerning pip: Please read our documentation, we have made it very clear we do not support pip since version 3.0 anymore!

blessyantony9

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issue commentdeeptools/HiCExplorer

Hicexplorer with Micro-C analysis

Maybe we can integrate it in a future release. However, don't expect a new release soon.

xl5525

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HiCExplorer 3.7.2 build 1 (#31877) * Remove biopython < 1.77 restriction * Update meta.yaml

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HiCExplorer 3.7.2 build 1

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Remove biopython 1.77 restriction

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PR opened bioconda/bioconda-recipes

HiCExplorer 3.7.2 build 1

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Remove biopython 1.77 restriction

Please read the guidelines for Bioconda recipes before opening a pull request (PR).

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Update meta.yaml

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Remove of Biopython (#31861) biopython is no longer a dependency in version 0.8.11

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Remove of Biopython

biopython is no longer a dependency in version 0.8.11

Describe your pull request here


Please read the guidelines for Bioconda recipes before opening a pull request (PR).

  • If this PR adds or updates a recipe, use "Add" or "Update" appropriately as the first word in its title.
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<details> <summary>Please use the following BiocondaBot commands:</summary>

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<table> <tr> <td><code>@BiocondaBot please update</code></td> <td>Merge the master branch into a PR.</td> </tr> <tr> <td><code>@BiocondaBot please add label</code></td> <td>Add the <code>please review & merge</code> label.</td> </tr> <tr> <td><code>@BiocondaBot please fetch artifacts</code></td> <td>Post links to CI-built packages/containers. <br />You can use this to test packages locally.</td> </tr> </table>

For members of the Bioconda project, the following command is also available:

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joachimwolff

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PR opened bioconda/bioconda-recipes

Remove of Biopython

biopython is no longer a dependency in version 0.8.11

Describe your pull request here


Please read the guidelines for Bioconda recipes before opening a pull request (PR).

  • If this PR adds or updates a recipe, use "Add" or "Update" appropriately as the first word in its title.
  • New recipes not directly relevant to the biological sciences need to be submitted to the conda-forge channel instead of Bioconda.
  • PRs require reviews prior to being merged. Once your PR is passing tests and ready to be merged, please issue the @BiocondaBot please add label command.
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<table> <tr> <td><code>@BiocondaBot please update</code></td> <td>Merge the master branch into a PR.</td> </tr> <tr> <td><code>@BiocondaBot please add label</code></td> <td>Add the <code>please review & merge</code> label.</td> </tr> <tr> <td><code>@BiocondaBot please fetch artifacts</code></td> <td>Post links to CI-built packages/containers. <br />You can use this to test packages locally.</td> </tr> </table>

For members of the Bioconda project, the following command is also available:

<table> <tr> <td><code>@BiocondaBot please merge</code></td> <td>Upload built packages/containers and merge a PR. <br />Someone must approve a PR first! <br />This reduces CI build time by reusing built artifacts.</td> </tr> </table>

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PR opened deeptools/HiCExplorer

Joachimwolff mamba
  • [ ] Flake8 passes (flake8 . --exclude=.venv,.build,planemo_test_env,build --ignore=E501,F403,E402,F999,F405,E712)
  • [ ] Local tests pass (py.test hicexplorer --doctest-modules)
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