Learning cell communication from spatial graphs of cells

Related tags

Deep Learningtensorflowglmcvaegcnencoder-decoder-modelgnnscanpysquidpy
Overview
Comments
  • Use Tangram mapped visium for ncem

    Use Tangram mapped visium for ncem

    Question Hello, Thank you for creating ncem. I wanted to ask if the Custom data loader also accepts tangram mapped adata. In specific: what should obsm node_types, proportions consist of ?

    question 
    opened by jkbenotmane 10
  • How to implement Input CODEX data for 'NCEM

    How to implement Input CODEX data for 'NCEM

    I am appreciated by your excellent work. I plan to use 'NCEM' package with my CODEX image data. Yet, I failed to load my data referring the tutorial code. I find there are a lot of prefix like 'zhang','Hartmann' to build a dataloader. I don't know how to choose them. May I request for a help?

    question 
    opened by Luosanj 9
  • DataLoader

    DataLoader

    Hi Anna and David,

    I am interested to apply ncem for one of the MERFISH data. But I do not understand how to make dataloader for this data. It would be very grateful if you can help me to built the initial inputs for the ncem then I can see what useful information I get from ncem. The link of data files are following. Thanks. https://www.dropbox.com/sh/w4c98xryzdjsffd/AACSCptc-0ekCeptCC9OLK32a?dl=0

    opened by ankitbioinfo 7
  • would ncem work on sequencing-based spatial transcriptomic data?

    would ncem work on sequencing-based spatial transcriptomic data?

    Question

    Hi, thank you for developing this great package. I am just wondering have you tried to run it on sequencing-based ST data, and do we need some special set up to make it work?

    question 
    opened by LuyiTian 4
  • Getting error in running python notebook of melc tonsils

    Getting error in running python notebook of melc tonsils

    Hi, I am running your example of following two notebooks data_exploration_melc_tonsils.ipynb, and model_benchmarks_melc_tonsils.ipynb In the first one I get the error at step "Supp. Fig. 7: Ligand–receptor permutation test"

    TypeError: init() got an unexpected keyword argument 'allowed_methods'

    And from the other notebook at step "Figure 1 (d): Modeling cell communication as spatial cell state dependencies"

    FileNotFoundError: [Errno 2] No such file or directory: '.210419_INTERACTIONS_BASELINE_NONE_NODES_PATIENT_1_pascualreguanttonsil/results/'

    Can you please let me know what I am missing here? Thanks.

    question 
    opened by ankitbioinfo 4
  • [DEPENDABOT]: Bump actions/cache from 2.1.6 to 3.2.1

    [DEPENDABOT]: Bump actions/cache from 2.1.6 to 3.2.1

    Bumps actions/cache from 2.1.6 to 3.2.1.

    Release notes

    Sourced from actions/cache's releases.

    v3.2.1

    What's Changed

    Full Changelog: https://github.com/actions/cache/compare/v3.2.0...v3.2.1

    v3.2.0

    What's Changed

    New Contributors

    Full Changelog: https://github.com/actions/cache/compare/v3...v3.2.0

    v3.2.0-beta.1

    What's Changed

    v3.1.0-beta.3

    What's Changed

    • Bug fixes for bsdtar fallback, if gnutar not available, and gzip fallback, if cache saved using old cache action, on windows.

    Full Changelog: https://github.com/actions/cache/compare/v3.1.0-beta.2...v3.1.0-beta.3

    ... (truncated)

    Changelog

    Sourced from actions/cache's changelog.

    3.2.1

    • Update @actions/cache on windows to use gnu tar and zstd by default and fallback to bsdtar and zstd if gnu tar is not available. (issue)
    • Added support for fallback to gzip to restore old caches on windows.
    • Added logs for cache version in case of a cache miss.
    Commits

    Dependabot compatibility score

    Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting @dependabot rebase.

    Dependabot commands and options

    You can trigger Dependabot actions by commenting on this PR:

    • @dependabot rebase will rebase this PR
    • @dependabot recreate will recreate this PR, overwriting any edits that have been made to it
    • @dependabot merge will merge this PR after your CI passes on it
    • @dependabot squash and merge will squash and merge this PR after your CI passes on it
    • @dependabot cancel merge will cancel a previously requested merge and block automerging
    • @dependabot reopen will reopen this PR if it is closed
    • @dependabot close will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
    • @dependabot ignore this major version will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)
    • @dependabot ignore this minor version will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)
    • @dependabot ignore this dependency will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)
    opened by dependabot[bot] 2
  • [DEPENDABOT]: Bump actions/cache from 2.1.6 to 3.2.0

    [DEPENDABOT]: Bump actions/cache from 2.1.6 to 3.2.0

    Bumps actions/cache from 2.1.6 to 3.2.0.

    Release notes

    Sourced from actions/cache's releases.

    v3.2.0

    What's Changed

    New Contributors

    Full Changelog: https://github.com/actions/cache/compare/v3...v3.2.0

    v3.2.0-beta.1

    What's Changed

    v3.1.0-beta.3

    What's Changed

    • Bug fixes for bsdtar fallback, if gnutar not available, and gzip fallback, if cache saved using old cache action, on windows.

    Full Changelog: https://github.com/actions/cache/compare/v3.1.0-beta.2...v3.1.0-beta.3

    v3.1.0-beta.2

    What's Changed

    Full Changelog: https://github.com/actions/cache/compare/v3.1.0-beta.1...v3.1.0-beta.2

    ... (truncated)

    Changelog

    Sourced from actions/cache's changelog.

    3.2.0

    • Released the two new actions - restore and save for granular control on cache
    Commits
    • c17f4bf GA for granular cache (#1035)
    • ac25611 docs: fix an invalid link in workarounds.md (#929)
    • dc097e3 Update examples.md (#1026)
    • fb86cbf Updated node example (#1008)
    • a57932f Merge pull request #1014 from jongwooo/chore/use-built-in-cache-action
    • 04b13ca chore: Use built-in cache action to cache dependencies
    • 941bc71 Merge pull request #1004 from jongwooo/chore/use-cache-in-check-dist
    • 08d8639 Merge branch 'main' into chore/use-cache-in-check-dist
    • a2f324e Merge pull request #1013 from jongwooo/refactor/use-early-return-pattern-to-a...
    • 35f4702 refactor: Use early return pattern to avoid nested conditions
    • Additional commits viewable in compare view

    Dependabot compatibility score

    Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting @dependabot rebase.

    Dependabot commands and options

    You can trigger Dependabot actions by commenting on this PR:

    • @dependabot rebase will rebase this PR
    • @dependabot recreate will recreate this PR, overwriting any edits that have been made to it
    • @dependabot merge will merge this PR after your CI passes on it
    • @dependabot squash and merge will squash and merge this PR after your CI passes on it
    • @dependabot cancel merge will cancel a previously requested merge and block automerging
    • @dependabot reopen will reopen this PR if it is closed
    • @dependabot close will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
    • @dependabot ignore this major version will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)
    • @dependabot ignore this minor version will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)
    • @dependabot ignore this dependency will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)
    opened by dependabot[bot] 2
  • [DEPENDABOT]: Bump actions/cache from 2.1.6 to 3.0.11

    [DEPENDABOT]: Bump actions/cache from 2.1.6 to 3.0.11

    Bumps actions/cache from 2.1.6 to 3.0.11.

    Release notes

    Sourced from actions/cache's releases.

    v3.0.11

    What's Changed

    New Contributors

    Full Changelog: https://github.com/actions/cache/compare/v3...v3.0.11

    v3.0.10

    • Fix a bug with sorting inputs.
    • Update definition for restore-keys in README.md

    v3.0.9

    • Enhanced the warning message for cache unavailability in case of GHES.

    v3.0.8

    What's Changed

    • Fix zstd not working for windows on gnu tar in issues.
    • Allow users to provide a custom timeout as input for aborting cache segment download using the environment variable SEGMENT_DOWNLOAD_TIMEOUT_MIN. Default is 60 minutes.

    v3.0.7

    What's Changed

    • Fix for the download stuck problem has been added in actions/cache for users who were intermittently facing the issue. As part of this fix, new timeout has been introduced in the download step to stop the download if it doesn't complete within an hour and run the rest of the workflow without erroring out.

    v3.0.6

    What's Changed

    • Add example for clojure lein project dependencies by @​shivamarora1 in PR actions/cache#835
    • Update toolkit's cache npm module to latest. Bump cache version to v3.0.6 by @​pdotl in PR actions/cache#887
    • Fix issue #809 where cache save/restore was failing for Amazon Linux 2 runners due to older tar version
    • Fix issue #833 where cache save was not working for caching github workspace directory

    New Contributors

    Full Changelog: https://github.com/actions/cache/compare/v3...v3.0.6

    v3.0.5

    Removed error handling by consuming actions/cache 3.0 toolkit, Now cache server error handling will be done by toolkit.

    v3.0.4

    In this release, we have fixed the tar creation error while trying to create it with path as ~/ home folder on ubuntu-latest.

    v3.0.3

    Fixed avoiding empty cache save when no files are available for caching. (actions/cache#624)

    v3.0.2

    ... (truncated)

    Changelog

    Sourced from actions/cache's changelog.

    3.0.11

    • Update toolkit version to 3.0.5 to include @actions/core@^1.10.0
    • Update @actions/cache to use updated saveState and setOutput functions from @actions/core@^1.10.0
    Commits
    • 9b0c1fc Merge pull request #956 from actions/pdotl-version-bump
    • 18103f6 Fix licensed status error
    • 3e383cd Update RELEASES
    • 43428ea toolkit versioon update and version bump for cache
    • 1c73980 3.0.11
    • a3f5edc Merge pull request #950 from rentziass/rentziass/update-actions-core
    • 831ee69 Update licenses
    • b9c8bfe Update @​actions/core to 1.10.0
    • 0f20846 Merge pull request #946 from actions/Phantsure-patch-2
    • 862fc14 Update README.md
    • Additional commits viewable in compare view

    Dependabot compatibility score

    Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting @dependabot rebase.

    Dependabot commands and options

    You can trigger Dependabot actions by commenting on this PR:

    • @dependabot rebase will rebase this PR
    • @dependabot recreate will recreate this PR, overwriting any edits that have been made to it
    • @dependabot merge will merge this PR after your CI passes on it
    • @dependabot squash and merge will squash and merge this PR after your CI passes on it
    • @dependabot cancel merge will cancel a previously requested merge and block automerging
    • @dependabot reopen will reopen this PR if it is closed
    • @dependabot close will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
    • @dependabot ignore this major version will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)
    • @dependabot ignore this minor version will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)
    • @dependabot ignore this dependency will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)
    opened by dependabot[bot] 2
  • [DEPENDABOT]: Bump actions/cache from 2.1.6 to 3.0.10

    [DEPENDABOT]: Bump actions/cache from 2.1.6 to 3.0.10

    Bumps actions/cache from 2.1.6 to 3.0.10.

    Release notes

    Sourced from actions/cache's releases.

    v3.0.10

    • Fix a bug with sorting inputs.
    • Update definition for restore-keys in README.md

    v3.0.9

    • Enhanced the warning message for cache unavailability in case of GHES.

    v3.0.8

    What's Changed

    • Fix zstd not working for windows on gnu tar in issues.
    • Allow users to provide a custom timeout as input for aborting cache segment download using the environment variable SEGMENT_DOWNLOAD_TIMEOUT_MIN. Default is 60 minutes.

    v3.0.7

    What's Changed

    • Fix for the download stuck problem has been added in actions/cache for users who were intermittently facing the issue. As part of this fix, new timeout has been introduced in the download step to stop the download if it doesn't complete within an hour and run the rest of the workflow without erroring out.

    v3.0.6

    What's Changed

    • Add example for clojure lein project dependencies by @​shivamarora1 in PR actions/cache#835
    • Update toolkit's cache npm module to latest. Bump cache version to v3.0.6 by @​pdotl in PR actions/cache#887
    • Fix issue #809 where cache save/restore was failing for Amazon Linux 2 runners due to older tar version
    • Fix issue #833 where cache save was not working for caching github workspace directory

    New Contributors

    Full Changelog: https://github.com/actions/cache/compare/v3...v3.0.6

    v3.0.5

    Removed error handling by consuming actions/cache 3.0 toolkit, Now cache server error handling will be done by toolkit.

    v3.0.4

    In this release, we have fixed the tar creation error while trying to create it with path as ~/ home folder on ubuntu-latest.

    v3.0.3

    Fixed avoiding empty cache save when no files are available for caching. (actions/cache#624)

    v3.0.2

    This release adds the support for dynamic cache size cap on GHES.

    v3.0.1

    • Added support for caching from GHES 3.5.
    • Fixed download issue for files > 2GB during restore.

    v3.0.0

    • This change adds a minimum runner version(node12 -> node16), which can break users using an out-of-date/fork of the runner. This would be most commonly affecting users on GHES 3.3 or before, as those runners do not support node16 actions and they can use actions from github.com via github connect or manually copying the repo to their GHES instance.

    • Few dependencies and cache action usage examples have also been updated.

    ... (truncated)

    Changelog

    Sourced from actions/cache's changelog.

    Releases

    3.0.0

    • Updated minimum runner version support from node 12 -> node 16

    3.0.1

    • Added support for caching from GHES 3.5.
    • Fixed download issue for files > 2GB during restore.

    3.0.2

    • Added support for dynamic cache size cap on GHES.

    3.0.3

    • Fixed avoiding empty cache save when no files are available for caching. (issue)

    3.0.4

    • Fixed tar creation error while trying to create tar with path as ~/ home folder on ubuntu-latest. (issue)

    3.0.5

    • Removed error handling by consuming actions/cache 3.0 toolkit, Now cache server error handling will be done by toolkit. (PR)

    3.0.6

    • Fixed #809 - zstd -d: no such file or directory error
    • Fixed #833 - cache doesn't work with github workspace directory

    3.0.7

    • Fixed #810 - download stuck issue. A new timeout is introduced in the download process to abort the download if it gets stuck and doesn't finish within an hour.

    3.0.8

    • Fix zstd not working for windows on gnu tar in issues #888 and #891.
    • Allowing users to provide a custom timeout as input for aborting download of a cache segment using an environment variable SEGMENT_DOWNLOAD_TIMEOUT_MIN. Default is 60 minutes.

    3.0.9

    • Enhanced the warning message for cache unavailablity in case of GHES.
    Commits

    Dependabot compatibility score

    Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting @dependabot rebase.

    Dependabot commands and options

    You can trigger Dependabot actions by commenting on this PR:

    • @dependabot rebase will rebase this PR
    • @dependabot recreate will recreate this PR, overwriting any edits that have been made to it
    • @dependabot merge will merge this PR after your CI passes on it
    • @dependabot squash and merge will squash and merge this PR after your CI passes on it
    • @dependabot cancel merge will cancel a previously requested merge and block automerging
    • @dependabot reopen will reopen this PR if it is closed
    • @dependabot close will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
    • @dependabot ignore this major version will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)
    • @dependabot ignore this minor version will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)
    • @dependabot ignore this dependency will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)
    opened by dependabot[bot] 2
  • [DEPENDABOT]: Bump actions/cache from 2.1.6 to 3.0.9

    [DEPENDABOT]: Bump actions/cache from 2.1.6 to 3.0.9

    Bumps actions/cache from 2.1.6 to 3.0.9.

    Release notes

    Sourced from actions/cache's releases.

    v3.0.9

    • Enhanced the warning message for cache unavailability in case of GHES.

    v3.0.8

    What's Changed

    • Fix zstd not working for windows on gnu tar in issues.
    • Allow users to provide a custom timeout as input for aborting cache segment download using the environment variable SEGMENT_DOWNLOAD_TIMEOUT_MIN. Default is 60 minutes.

    v3.0.7

    What's Changed

    • Fix for the download stuck problem has been added in actions/cache for users who were intermittently facing the issue. As part of this fix, new timeout has been introduced in the download step to stop the download if it doesn't complete within an hour and run the rest of the workflow without erroring out.

    v3.0.6

    What's Changed

    • Add example for clojure lein project dependencies by @​shivamarora1 in PR actions/cache#835
    • Update toolkit's cache npm module to latest. Bump cache version to v3.0.6 by @​pdotl in PR actions/cache#887
    • Fix issue #809 where cache save/restore was failing for Amazon Linux 2 runners due to older tar version
    • Fix issue #833 where cache save was not working for caching github workspace directory

    New Contributors

    Full Changelog: https://github.com/actions/cache/compare/v3...v3.0.6

    v3.0.5

    Removed error handling by consuming actions/cache 3.0 toolkit, Now cache server error handling will be done by toolkit.

    v3.0.4

    In this release, we have fixed the tar creation error while trying to create it with path as ~/ home folder on ubuntu-latest.

    v3.0.3

    Fixed avoiding empty cache save when no files are available for caching. (actions/cache#624)

    v3.0.2

    This release adds the support for dynamic cache size cap on GHES.

    v3.0.1

    • Added support for caching from GHES 3.5.
    • Fixed download issue for files > 2GB during restore.

    v3.0.0

    • This change adds a minimum runner version(node12 -> node16), which can break users using an out-of-date/fork of the runner. This would be most commonly affecting users on GHES 3.3 or before, as those runners do not support node16 actions and they can use actions from github.com via github connect or manually copying the repo to their GHES instance.

    • Few dependencies and cache action usage examples have also been updated.

    v2.1.7

    Support 10GB cache upload using the latest version 1.0.8 of @actions/cache

    Changelog

    Sourced from actions/cache's changelog.

    3.0.9

    • Enhanced the warning message for cache unavailablity in case of GHES.
    Commits

    Dependabot compatibility score

    Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting @dependabot rebase.

    Dependabot commands and options

    You can trigger Dependabot actions by commenting on this PR:

    • @dependabot rebase will rebase this PR
    • @dependabot recreate will recreate this PR, overwriting any edits that have been made to it
    • @dependabot merge will merge this PR after your CI passes on it
    • @dependabot squash and merge will squash and merge this PR after your CI passes on it
    • @dependabot cancel merge will cancel a previously requested merge and block automerging
    • @dependabot reopen will reopen this PR if it is closed
    • @dependabot close will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
    • @dependabot ignore this major version will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)
    • @dependabot ignore this minor version will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)
    • @dependabot ignore this dependency will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)
    opened by dependabot[bot] 2
  • [DEPENDABOT]: Bump actions/setup-python from 2.1.4 to 4.2.0

    [DEPENDABOT]: Bump actions/setup-python from 2.1.4 to 4.2.0

    Bumps actions/setup-python from 2.1.4 to 4.2.0.

    Release notes

    Sourced from actions/setup-python's releases.

    Add check-latest input and bug fixes

    In scope of this release we add the check-latest input. If check-latest is set to true, the action first checks if the cached version is the latest one. If the locally cached version is not the most up-to-date, the version will then be downloaded from python-versions repository. By default check-latest is set to false. For PyPy it will to try to reach https://downloads.python.org/pypy/versions.json

    Example of usage:

    steps:
  - uses: actions/[email protected]
  - uses: actions/[email protected]
    with:
      python-version: '3.9'
      check-latest: true
  - run: python --version

    Besides, it includes such changes as

    v4.1.0

    In scope of this pull request we updated actions/cache package as the new version contains fixes for caching error handling. Moreover, we added a new input update-environment. This option allows to specify if the action shall update environment variables (default) or not.

    Update-environment input

        - name: setup-python 3.9
      uses: actions/[email protected]
      with:
        python-version: 3.9
        update-environment: false

    Besides, we added such changes as:

    v4.0.0

    What's Changed

    • Support for python-version-file input: #336

    Example of usage:

    - uses: actions/[email protected]
  with:
    python-version-file: '.python-version' # Read python version from a file
- run: python my_script.py
</tr></table>

    ... (truncated)

    Commits

    Dependabot compatibility score

    Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting @dependabot rebase.

    Dependabot commands and options

    You can trigger Dependabot actions by commenting on this PR:

    • @dependabot rebase will rebase this PR
    • @dependabot recreate will recreate this PR, overwriting any edits that have been made to it
    • @dependabot merge will merge this PR after your CI passes on it
    • @dependabot squash and merge will squash and merge this PR after your CI passes on it
    • @dependabot cancel merge will cancel a previously requested merge and block automerging
    • @dependabot reopen will reopen this PR if it is closed
    • @dependabot close will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
    • @dependabot ignore this major version will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)
    • @dependabot ignore this minor version will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)
    • @dependabot ignore this dependency will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)
    opened by dependabot[bot] 2
  • [DEPENDABOT]: Bump actions/cache from 2.1.6 to 3.2.2

    [DEPENDABOT]: Bump actions/cache from 2.1.6 to 3.2.2

    Bumps actions/cache from 2.1.6 to 3.2.2.

    Release notes

    Sourced from actions/cache's releases.

    v3.2.2

    What's Changed

    New Contributors

    Full Changelog: https://github.com/actions/cache/compare/v3.2.1...v3.2.2

    v3.2.1

    What's Changed

    Full Changelog: https://github.com/actions/cache/compare/v3.2.0...v3.2.1

    v3.2.0

    What's Changed

    New Contributors

    ... (truncated)

    Changelog

    Sourced from actions/cache's changelog.

    3.2.2

    • Reverted the changes made in 3.2.1 to use gnu tar and zstd by default on windows.
    Commits
    • 4723a57 Revert compression changes related to windows but keep version logging (#1049)
    • d1507cc Merge pull request #1042 from me-and/correct-readme-re-windows
    • 3337563 Merge branch 'main' into correct-readme-re-windows
    • 60c7666 save/README.md: Fix typo in example (#1040)
    • b053f2b Fix formatting error in restore/README.md (#1044)
    • 501277c README.md: remove outdated Windows cache tip link
    • c1a5de8 Upgrade codeql to v2 (#1023)
    • 9b0be58 Release compression related changes for windows (#1039)
    • c17f4bf GA for granular cache (#1035)
    • ac25611 docs: fix an invalid link in workarounds.md (#929)
    • Additional commits viewable in compare view

    Dependabot compatibility score

    Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting @dependabot rebase.

    Dependabot commands and options

    You can trigger Dependabot actions by commenting on this PR:

    • @dependabot rebase will rebase this PR
    • @dependabot recreate will recreate this PR, overwriting any edits that have been made to it
    • @dependabot merge will merge this PR after your CI passes on it
    • @dependabot squash and merge will squash and merge this PR after your CI passes on it
    • @dependabot cancel merge will cancel a previously requested merge and block automerging
    • @dependabot reopen will reopen this PR if it is closed
    • @dependabot close will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
    • @dependabot ignore this major version will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)
    • @dependabot ignore this minor version will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)
    • @dependabot ignore this dependency will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)
    opened by dependabot[bot] 1
  • [DEPENDABOT]: Bump pre-commit from 2.12.0 to 2.21.0

    [DEPENDABOT]: Bump pre-commit from 2.12.0 to 2.21.0

    Bumps pre-commit from 2.12.0 to 2.21.0.

    Release notes

    Sourced from pre-commit's releases.

    pre-commit v2.21.0

    Features

    Fixes

    pre-commit v2.20.0

    Features

    • Expose source and object-name (positional args) of prepare-commit-msg hook as PRE_COMMIT_COMIT_MSG_SOURCE and PRE_COMMIT_COMMIT_OBJECT_NAME.

    Fixes

    ... (truncated)

    Changelog

    Sourced from pre-commit's changelog.

    2.21.0 - 2022-12-25

    Features

    Fixes

    2.20.0 - 2022-07-10

    Features

    • Expose source and object-name (positional args) of prepare-commit-msg hook as PRE_COMMIT_COMIT_MSG_SOURCE and PRE_COMMIT_COMMIT_OBJECT_NAME.

    Fixes

    ... (truncated)

    Commits
    • 40c5bda v2.21.0
    • bb27ea3 Merge pull request #2642 from rkm/fix/dotnet-nuget-config
    • c38e0c7 dotnet: ignore nuget source during tool install
    • bce513f Merge pull request #2641 from rkm/fix/dotnet-tool-prefix
    • e904628 fix dotnet hooks with prefixes
    • d7b8b12 Merge pull request #2646 from pre-commit/pre-commit-ci-update-config
    • 94b6178 [pre-commit.ci] pre-commit autoupdate
    • b474a83 Merge pull request #2643 from pre-commit/pre-commit-ci-update-config
    • a179808 [pre-commit.ci] pre-commit autoupdate
    • 3aa6206 Merge pull request #2605 from lorenzwalthert/r/fix-exe
    • Additional commits viewable in compare view

    Dependabot compatibility score

    Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting @dependabot rebase.

    Dependabot commands and options

    You can trigger Dependabot actions by commenting on this PR:

    • @dependabot rebase will rebase this PR
    • @dependabot recreate will recreate this PR, overwriting any edits that have been made to it
    • @dependabot merge will merge this PR after your CI passes on it
    • @dependabot squash and merge will squash and merge this PR after your CI passes on it
    • @dependabot cancel merge will cancel a previously requested merge and block automerging
    • @dependabot reopen will reopen this PR if it is closed
    • @dependabot close will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
    • @dependabot ignore this major version will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)
    • @dependabot ignore this minor version will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)
    • @dependabot ignore this dependency will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)
    opened by dependabot[bot] 1
  • [DEPENDABOT]: Bump pre-commit-hooks from 3.4.0 to 4.4.0

    [DEPENDABOT]: Bump pre-commit-hooks from 3.4.0 to 4.4.0

    Bumps pre-commit-hooks from 3.4.0 to 4.4.0.

    Release notes

    Sourced from pre-commit-hooks's releases.

    pre-commit-hooks v4.3.0

    Features

    • check-executables-have-shebangs: use git config core.fileMode to determine if it should query git.
    • name-tests-test: add --pytest-test-first test convention.

    Fixes

    pre-commit-hooks v4.2.0

    Features

    Fixes

    • check-merge-conflict: fix detection of ====== conflict marker on windows.

    Updating

    pre-commit-hooks v4.1.0

    Features

    ... (truncated)

    Changelog

    Sourced from pre-commit-hooks's changelog.

    4.4.0 - 2022-11-23

    Features

    4.3.0 - 2022-06-07

    Features

    • check-executables-have-shebangs: use git config core.fileMode to determine if it should query git.
    • name-tests-test: add --pytest-test-first test convention.

    Fixes

    4.2.0 - 2022-04-06

    Features

    Fixes

    • check-merge-conflict: fix detection of ====== conflict marker on windows.

    Updating

    • Drop python<3.7.
    • Changed default branch from master to main.

    ... (truncated)

    Commits
    • f71fa2c v4.4.0
    • afb705d Merge pull request #841 from pre-commit/pre-commit-ci-update-config
    • a63d8f3 [pre-commit.ci] pre-commit autoupdate
    • b4982b5 Merge pull request #840 from pre-commit/all-repos_autofix_no-implicit-optional
    • 360df52 remove no_implicit_optional
    • 5d205e6 Merge pull request #838 from pre-commit/pre-commit-ci-update-config
    • c44770d [pre-commit.ci] pre-commit autoupdate
    • c032263 Merge pull request #829 from pre-commit/pre-commit-ci-update-config
    • 0a7d3b7 [pre-commit.ci] pre-commit autoupdate
    • 4dcb74a Merge pull request #822 from pre-commit/pre-commit-ci-update-config
    • Additional commits viewable in compare view

    Dependabot compatibility score

    Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting @dependabot rebase.

    Dependabot commands and options

    You can trigger Dependabot actions by commenting on this PR:

    • @dependabot rebase will rebase this PR
    • @dependabot recreate will recreate this PR, overwriting any edits that have been made to it
    • @dependabot merge will merge this PR after your CI passes on it
    • @dependabot squash and merge will squash and merge this PR after your CI passes on it
    • @dependabot cancel merge will cancel a previously requested merge and block automerging
    • @dependabot reopen will reopen this PR if it is closed
    • @dependabot close will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
    • @dependabot ignore this major version will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)
    • @dependabot ignore this minor version will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)
    • @dependabot ignore this dependency will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)
    opened by dependabot[bot] 1
  • Supporting jinja2>=3.0.3

    Supporting jinja2>=3.0.3

    I have a problem with installing ncem in my virtual environment.

    My environment is pre-installed with jupyterlab-server 2.11.2 requiring jinja2>=3.0.3. When I tried to install ncem, I received an error message stating that it requires jinja2<3.0.0,>=2.11.3.

    **Could you please update ncem to support Jinja2>=3.0.3? **

    enhancement 
    opened by GaoGN 0
  • How to run NCEM for CODEX csv/or FCS output data?

    How to run NCEM for CODEX csv/or FCS output data?

    Question

    Hi I want to use NCEM for CODEX data , but I could find any tutorial or how to prepare the data for this type of analysis.

    Could please direct me if there is any tutorial or notebook that you could share with us ?

    question 
    opened by DRSEI 0
  • Issue installing ncem on macOS

    Issue installing ncem on macOS

    I am trying to install ncem on my machine: macOS Monterey 12.6.1 pip 22.2.2 from /Users/sei/opt/miniconda3/envs/test-env/lib/python3.8/site-packages/pip (python 3.8)

    pip install ncem

    When I do this I get the following error:

    (test-env) [email protected] ~ % pip install ncem

Collecting ncem
  Using cached ncem-0.1.4-py3-none-any.whl (119 kB)
Collecting click<8.0.0,>=7.1.2
  Using cached click-7.1.2-py2.py3-none-any.whl (82 kB)
Collecting patsy<0.6.0,>=0.5.1
  Using cached patsy-0.5.3-py2.py3-none-any.whl (233 kB)
Collecting Jinja2<4.0.0,>=2.11.3
  Using cached Jinja2-3.1.2-py3-none-any.whl (133 kB)
Collecting docrep<0.4.0,>=0.3.2
  Using cached docrep-0.3.2.tar.gz (33 kB)
  Preparing metadata (setup.py) ... done
Collecting matplotlib<4.0.0,>=3.4.2
  Using cached matplotlib-3.6.1-cp38-cp38-macosx_11_0_arm64.whl (7.2 MB)
Collecting diffxpy<0.8.0,>=0.7.4
  Using cached diffxpy-0.7.4-py3-none-any.whl (85 kB)
Collecting scipy<2.0.0,>=1.7.0
  Using cached scipy-1.9.3-cp38-cp38-macosx_12_0_arm64.whl (28.5 MB)
Collecting scanpy<2.0.0,>=1.7.2
  Using cached scanpy-1.9.1-py3-none-any.whl (2.0 MB)
Collecting squidpy<2.0.0,>=1.0.0
  Using cached squidpy-1.2.3-py3-none-any.whl (180 kB)
Collecting PyYAML<6.0.0,>=5.4.1
  Using cached PyYAML-5.4.1.tar.gz (175 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting louvain<0.8.0,>=0.7.0
  Using cached louvain-0.7.2-cp38-cp38-macosx_11_0_arm64.whl (187 kB)
Collecting rich<11.0.0,>=10.1.0
  Using cached rich-10.16.2-py3-none-any.whl (214 kB)
Collecting ncem
  Using cached ncem-0.1.3-py3-none-any.whl (118 kB)
  Using cached ncem-0.1.2-py3-none-any.whl (117 kB)
  Using cached ncem-0.1.1-py3-none-any.whl (105 kB)
  Using cached ncem-0.1.0-py3-none-any.whl (82 kB)
Collecting Jinja2<3.0.0,>=2.11.3
  Using cached Jinja2-2.11.3-py2.py3-none-any.whl (125 kB)
ERROR: Cannot install ncem==0.1.0, ncem==0.1.1, ncem==0.1.2, ncem==0.1.3 and ncem==0.1.4 because these package versions have conflicting dependencies.

The conflict is caused by:
    ncem 0.1.4 depends on tensorflow<3.0.0 and >=2.5.0
    ncem 0.1.3 depends on tensorflow<3.0.0 and >=2.5.0
    ncem 0.1.2 depends on tensorflow<3.0.0 and >=2.5.0
    ncem 0.1.1 depends on tensorflow<3.0.0 and >=2.5.0
    ncem 0.1.0 depends on tensorflow<3.0.0 and >=2.5.0

To fix this you could try to:
1. loosen the range of package versions you've specified
2. remove package versions to allow pip attempt to solve the dependency conflict

ERROR: ResolutionImpossible: for help visit https://pip.pypa.io/en/latest/topics/dependency-resolution/#dealing-with-dependency-conflicts

    Please let me know if there's anything else I should be doing beforehand. Thank you kindly for your help

    opened by DRSEI 0
Releases(0.1.4)

  • 0.1.4(Aug 8, 2022)

  • 0.1.3(May 18, 2022)

  • 0.1.2(Mar 23, 2022)

    What's Changed

    • Feature/simulation by @davidsebfischer in https://github.com/theislab/ncem/pull/60
    • Feature/simulation by @AnnaChristina in https://github.com/theislab/ncem/pull/62
    • [DEPENDABOT]: Bump scanpy from 1.7.2 to 1.8.2 by @dependabot in https://github.com/theislab/ncem/pull/55
    • [DEPENDABOT]: Bump pygments from 2.8.1 to 2.11.2 by @dependabot in https://github.com/theislab/ncem/pull/68
    • [DEPENDABOT]: Bump codecov/codecov-action from 2.0.3 to 2.1.0 by @dependabot in https://github.com/theislab/ncem/pull/43
    • Deconv visium by @AnnaChristina in https://github.com/theislab/ncem/pull/70
    • add example cell radius to plot by @AnnaChristina in https://github.com/theislab/ncem/pull/79

    Full Changelog: https://github.com/theislab/ncem/compare/0.1.1...0.1.2

    Source code(tar.gz)
    Source code(zip)

  • 0.1.1(Nov 18, 2021)

  • v0.1.0(Jul 2, 2021)

Owner
Theis Lab
Institute of Computational Biology
Theis Lab
GitHub Repository https://ncem.readthedocs.io/
This is the paddle code for SeBoW(Self-Born wiring for neural trees), a kind of neural tree born form a large search space

SeBoW: Self-Born Wiring for neural trees(PaddlePaddle version) This is the paddle code for SeBoW(Self-Born wiring for neural trees), a kind of neural

HollyLee 13 Dec 08, 2022
A framework for the elicitation, specification, formalization and understanding of requirements.

A framework for the elicitation, specification, formalization and understanding of requirements.

NASA - Software V&V 161 Jan 03, 2023
VSR-Transformer - This paper proposes a new Transformer for video super-resolution (called VSR-Transformer).

VSR-Transformer By Jiezhang Cao, Yawei Li, Kai Zhang, Luc Van Gool This paper proposes a new Transformer for video super-resolution (called VSR-Transf

Jiezhang Cao 225 Nov 13, 2022
Few-Shot Graph Learning for Molecular Property Prediction

Few-shot Graph Learning for Molecular Property Prediction Introduction This is the source code and dataset for the following paper: Few-shot Graph Lea

Zhichun Guo 94 Dec 12, 2022
A modified version of DeepMind's Alphafold2 to divide CPU part (MSA and template searching) and GPU part (prediction model)

ParallelFold Author: Bozitao Zhong This is a modified version of DeepMind's Alphafold2 to divide CPU part (MSA and template searching) and GPU part (p

Bozitao Zhong 77 Dec 22, 2022
Low-code/No-code approach for deep learning inference on devices

EzEdgeAI A concept project that uses a low-code/no-code approach to implement deep learning inference on devices. It provides a componentized framewor

On-Device AI Co., Ltd. 7 Apr 05, 2022
Pytorch Implementation of Zero-Shot Image-to-Text Generation for Visual-Semantic Arithmetic

Pytorch Implementation of Zero-Shot Image-to-Text Generation for Visual-Semantic Arithmetic [Paper] [Colab is coming soon] Approach Example Usage To r

170 Jan 03, 2023
Scales, Chords, and Cadences: Practical Music Theory for MIR Researchers

ISMIR-musicTheoryTutorial This repository has slides and Jupyter notebooks for the ISMIR 2021 tutorial Scales, Chords, and Cadences: Practical Music T

Johanna Devaney 58 Oct 11, 2022
Pytorch port of Google Research's LEAF Audio paper

leaf-audio-pytorch Pytorch port of Google Research's LEAF Audio paper published at ICLR 2021. This port is not completely finished, but the Leaf() fro

Dennis Fedorishin 80 Oct 31, 2022
IRON Kaggle project done while doing IRONHACK Bootcamp where we had to analyze and use a Machine Learning Project to predict future sales

IRON Kaggle project done while doing IRONHACK Bootcamp where we had to analyze and use a Machine Learning Project to predict future sales. In this case, we ended up using XGBoost because it was the o

1 Jan 04, 2022
TensorFlow Metal Backend on Apple Silicon Experiments (just for fun)

tf-metal-experiments TensorFlow Metal Backend on Apple Silicon Experiments (just for fun) Setup This is tested on M1 series Apple Silicon SOC only. Te

Timothy Liu 161 Jan 03, 2023
DeepDiffusion: Unsupervised Learning of Retrieval-adapted Representations via Diffusion-based Ranking on Latent Feature Manifold

DeepDiffusion Introduction This repository provides the code of the DeepDiffusion algorithm for unsupervised learning of retrieval-adapted representat

4 Nov 15, 2022
Activating More Pixels in Image Super-Resolution Transformer

HAT [Paper Link] Activating More Pixels in Image Super-Resolution Transformer Xiangyu Chen, Xintao Wang, Jiantao Zhou and Chao Dong BibTeX @article{ch

XyChen 270 Dec 27, 2022
A toy compiler that can convert Python scripts to pickle bytecode 🥒

Pickora 🐰 A small compiler that can convert Python scripts to pickle bytecode. Requirements Python 3.8+ No third-party modules are required. Usage us

ꌗᖘ꒒ꀤ꓄꒒ꀤꈤꍟ 68 Jan 04, 2023
A Sign Language detection project using Mediapipe landmark detection and Tensorflow LSTM's

sign-language-detection A Sign Language detection project using Mediapipe landmark detection and Tensorflow LSTM. The project is built for a vocabular

Hashim 4 Feb 06, 2022
U-Net Brain Tumor Segmentation

U-Net Brain Tumor Segmentation 🚀 ：Feb 2019 the data processing implementation in this repo is not the fastest way (code need update, contribution is

Hao 448 Jan 02, 2023
CTF Challenge for CSAW Finals 2021

Terminal Velocity Misc CTF Challenge for CSAW Finals 2021 This is a challenge I've had in mind for almost 15 years and never got around to building un

Jordan 6 Jul 30, 2022
Face Detection & Age Gender & Expression & Recognition

Face Detection & Age Gender & Expression & Recognition

Sajjad Ayobi 188 Dec 28, 2022
Transformer Tracking (CVPR2021)

TransT - Transformer Tracking [CVPR2021] Official implementation of the TransT (CVPR2021) , including training code and trained models. We are revisin

chenxin 465 Jan 06, 2023
This repository implements and evaluates convolutional networks on the Möbius strip as toy model instantiations of Coordinate Independent Convolutional Networks.

Orientation independent Möbius CNNs This repository implements and evaluates convolutional networks on the Möbius strip as toy model instantiations of

Maurice Weiler 59 Dec 09, 2022