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/
Flexible time series feature extraction & processing

tsflex is a toolkit for flexible time series processing & feature extraction, that is efficient and makes few assumptions about sequence data. Useful

PreDiCT.IDLab 206 Dec 28, 2022
Data pipelines for both TensorFlow and PyTorch!

rapidnlp-datasets Data pipelines for both TensorFlow and PyTorch ! If you want to load public datasets, try: tensorflow/datasets huggingface/datasets

1 Dec 08, 2021
K-FACE Analysis Project on Pytorch

Installation Setup with Conda # create a new environment conda create --name insightKface python=3.7 # or over conda activate insightKface #install t

Jung Jun Uk 7 Nov 10, 2022
Bayesian dessert for Lasagne

Gelato Bayesian dessert for Lasagne Recent results in Bayesian statistics for constructing robust neural networks have proved that it is one of the be

Maxim Kochurov 84 May 11, 2020
This is the official released code for our paper, The Emergence of Objectness: Learning Zero-Shot Segmentation from Videos

The-Emergence-of-Objectness This is the official released code for our paper, The Emergence of Objectness: Learning Zero-Shot Segmentation from Videos

44 Oct 08, 2022
This codebase is the official implementation of Test-Time Classifier Adjustment Module for Model-Agnostic Domain Generalization (NeurIPS2021, Spotlight)

Test-Time Classifier Adjustment Module for Model-Agnostic Domain Generalization This codebase is the official implementation of Test-Time Classifier A

47 Dec 28, 2022
Heterogeneous Deep Graph Infomax

Heterogeneous-Deep-Graph-Infomax Parameter Setting: HDGI-A: Node-level dimension: 16 Attention head: 4 Semantic-level attention vector: 8 learning rat

52 Oct 31, 2022
TGRNet: A Table Graph Reconstruction Network for Table Structure Recognition

TGRNet: A Table Graph Reconstruction Network for Table Structure Recognition Xue, Wenyuan, et al. "TGRNet: A Table Graph Reconstruction Network for Ta

Wenyuan 68 Jan 04, 2023
Self-attentive task GAN for space domain awareness data augmentation.

SATGAN TODO: update the article URL once published. Article about this implemention The self-attentive task generative adversarial network (SATGAN) le

Nathan 2 Mar 24, 2022
Code for our paper "Graph Pre-training for AMR Parsing and Generation" in ACL2022

AMRBART An implementation for ACL2022 paper "Graph Pre-training for AMR Parsing and Generation". You may find our paper here (Arxiv). Requirements pyt

xfbai 60 Jan 03, 2023
Evidential Softmax for Sparse Multimodal Distributions in Deep Generative Models

Evidential Softmax for Sparse Multimodal Distributions in Deep Generative Models Abstract Many applications of generative models rely on the marginali

Stanford Intelligent Systems Laboratory 9 Jun 06, 2022
[NeurIPS 2020] Code for the paper "Balanced Meta-Softmax for Long-Tailed Visual Recognition"

Balanced Meta-Softmax Code for the paper Balanced Meta-Softmax for Long-Tailed Visual Recognition Jiawei Ren, Cunjun Yu, Shunan Sheng, Xiao Ma, Haiyu

Jiawei Ren 65 Dec 21, 2022
The object detection pipeline is based on Ultralytics YOLOv5

AYOLOv2 The main goal of this repository is to rewrite the object detection pipeline with a better code structure for better portability and adaptabil

153 Dec 22, 2022
Parameterising Simulated Annealing for the Travelling Salesman Problem

Parameterising Simulated Annealing for the Travelling Salesman Problem

Gary Sun 55 Jun 15, 2022
Facial detection, landmark tracking and expression transfer library for Windows, Linux and Mac

Welcome to the CSIRO Face Analysis SDK. Documentation for the SDK can be found in doc/documentation.html. All code in this SDK is provided according t

Luiz Carlos Vieira 7 Jul 16, 2020
Generic Foreground Segmentation in Images

Pixel Objectness The following repository contains pretrained model for pixel objectness. Please visit our project page for the paper and visual resul

Suyog Jain 157 Nov 21, 2022
Finetuning Pipeline

KLUE Baseline Korean(한국어) KLUE-baseline contains the baseline code for the Korean Language Understanding Evaluation (KLUE) benchmark. See our paper fo

74 Dec 13, 2022
Implementation of Convolutional LSTM in PyTorch.

ConvLSTM_pytorch This file contains the implementation of Convolutional LSTM in PyTorch made by me and DavideA. We started from this implementation an

Andrea Palazzi 1.3k Dec 29, 2022
NasirKhusraw - The TSP solved using genetic algorithm and show TSP path overlaid on a map of the Iran provinces & their capitals.

Nasir Khusraw : Travelling Salesman Problem The TSP solved using genetic algorithm. This project show TSP path overlaid on a map of the Iran provinces

J Brave 2 Sep 01, 2022
A light and fast one class detection framework for edge devices. We provide face detector, head detector, pedestrian detector, vehicle detector......

A Light and Fast Face Detector for Edge Devices Big News: LFD, which is a big update of LFFD, now is released (2021.03.09). It is strongly recommended

YonghaoHe 1.3k Dec 25, 2022