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ModsDr. Alex M. Mawla, PhD

encode-toolkit Plugin

20 ENCODE API tools + 47 expert skills for genomics research. Search experiments, download files with MD5 verification, run pipelines, and cross-reference 14 databases.

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Only the newest 50 observations in this subscription, not a full archive, upstream releases or installs. Updates-page links keep observation type and package filters; package-page links include all kinds for that package. Your local following list is not sent.

Install

This version is listed in the verified marketplace ammawla (repository ammawla/encode-toolkit). Run these in Claude Code, in order:

  1. Add the marketplace/plugin marketplace add ammawla/encode-toolkit
  2. Install the plugin/plugin install encode-toolkit@ammawla

These commands install the marketplace's current upstream state, not the pinned commit snapshot on this page; the two can differ.

Contents of latest version 0.3.4 (commit 36836c8)

Contents 65

Skill47
Agent7
Command10
MCP server1
Dependencies, compatibility and skill declarations

Recorded dependencies 0

No dependency requirements were recorded from plugin.json or marketplace entries. Only manifest fields saved with the snapshot are shown here; dependency declarations in other files are outside the current collection scope.

Recorded compatibility

No compatibility requirement was recorded for this snapshot from plugin.json or a marketplace entry. Only manifest fields saved with the snapshot are shown here. Declarations in a skill's SKILL.md header are collected separately and, when present, shown on their own under “Skill file declarations”; they never overwrite or fill in this value.

Skill file declarations 47

The content below was read separately from the header of each skill file (SKILL.md) at its pinned commit. It is text the file declares about itself, shown as an annotation only. It is stored apart from the snapshot's dependencies and compatibility (manifest fields) above and does not overwrite them. It is not the package license, version, install count or a release record, and none of it is verified.

Evidence scope and limits
  • Each entry is one file at one pinned commit, and field states hold for that file only. Components that point to the same file are merged into one entry; files with identical content share one extraction.
  • “Declared in file” means the file's header has the field. “Not declared in this file” appears only when the header parsed successfully and lacks the field. “Invalid declaration” means the field is present but its type, length or characters do not meet the requirements; it is never rewritten or truncated. “Not read” means no usable header was obtained (not yet read, read failed, no header, or an unparseable header), which says neither that the field was declared nor that it was not.
  • Compatibility and license text are the file's own wording. They do not show that anything runs, are not legal advice, and are not a license verification. metadata.version is only an annotation inside the file; it is not the package version and is not used to judge which is newer.
  • This list groups the version's skill components by their recorded source. A listed source may still be unpinned, unread or unavailable; each entry shows its state. Collection runs in bounded batches and does not promise complete coverage.
  • A file whose read failed shows a “retry eligible” time. It is only when the collector may try again, not a schedule, and it does not promise a read or completion.

1–20 of 47 skill file sources · As of

  1. plugin/skills/accessibility-aggregation/SKILL.md

    Header parsed

    Components using this file 1

    • accessibility-aggregation plugin/skills/accessibility-aggregation/SKILL.md

    Fields declared in the file

    Compatibility (declared in file)
    Not declared in this fileThe header parsed and has no such field; true for this file only.
    License text (declared in file, unverified)
    Not declared in this fileThe header parsed and has no such field; true for this file only.
    metadata.version (file annotation)
    Not declared in this fileThe header parsed and has no such field; true for this file only.
    Repository
    ammawla/encode-toolkit
    Pinned commit
    36836c8725fd4d20d9c851ce314f5151aea5f57c
    File identity
    Regular-file identity recorded
    Blob SHA
    04557ab75996c8e1a12c19bfc0725e1759c4c9b9
    Mode
    100644
    Identity recorded
    Header parse
    Header parsed

    Extraction record

    First extracted by extractor version 1.

    First read from
    The same file as above.

  2. plugin/skills/batch-analysis/SKILL.md

    Header parsed

    Components using this file 1

    • batch-analysis plugin/skills/batch-analysis/SKILL.md

    Fields declared in the file

    Compatibility (declared in file)
    Not declared in this fileThe header parsed and has no such field; true for this file only.
    License text (declared in file, unverified)
    Not declared in this fileThe header parsed and has no such field; true for this file only.
    metadata.version (file annotation)
    Not declared in this fileThe header parsed and has no such field; true for this file only.
    Repository
    ammawla/encode-toolkit
    Pinned commit
    36836c8725fd4d20d9c851ce314f5151aea5f57c
    File identity
    Regular-file identity recorded
    Blob SHA
    64deeb54b1b1d8e142a0e80554933e55f2e3e6ca
    Mode
    100644
    Identity recorded
    Header parse
    Header parsed

    Extraction record

    First extracted by extractor version 1.

    First read from
    The same file as above.

  3. plugin/skills/bioinformatics-installer/SKILL.md

    Not read

    Components using this file 1

    • bioinformatics-installer plugin/skills/bioinformatics-installer/SKILL.md

    Fields declared in the file

    Compatibility (declared in file)
    Not readNo usable header, which says neither that it was declared nor that it was not.
    License text (declared in file, unverified)
    Not readNo usable header, which says neither that it was declared nor that it was not.
    metadata.version (file annotation)
    Not readNo usable header, which says neither that it was declared nor that it was not.

    This file has no usable extraction record yet, so all three fields show as “Not read”.

    Repository
    ammawla/encode-toolkit
    Pinned commit
    36836c8725fd4d20d9c851ce314f5151aea5f57c
    File identity
    Regular-file identity recorded
    Blob SHA
    b41e3adb5c881946a260a6980eb44df2c6b5a289
    Mode
    100644
    Identity recorded
    Header parse
    Not read
    Why not read
    The file identity is recorded, but its content has not been read yet. declaration_unread

    No extraction record yet.

  4. plugin/skills/cellxgene-context/SKILL.md

    Not read

    Components using this file 1

    • cellxgene-context plugin/skills/cellxgene-context/SKILL.md

    Fields declared in the file

    Compatibility (declared in file)
    Not readNo usable header, which says neither that it was declared nor that it was not.
    License text (declared in file, unverified)
    Not readNo usable header, which says neither that it was declared nor that it was not.
    metadata.version (file annotation)
    Not readNo usable header, which says neither that it was declared nor that it was not.

    This file has no usable extraction record yet, so all three fields show as “Not read”.

    Repository
    ammawla/encode-toolkit
    Pinned commit
    36836c8725fd4d20d9c851ce314f5151aea5f57c
    File identity
    Regular-file identity recorded
    Blob SHA
    79de49419530ca1f52e879cde9516b30c32259ad
    Mode
    100644
    Identity recorded
    Header parse
    Not read
    Why not read
    The file identity is recorded, but its content has not been read yet. declaration_unread

    No extraction record yet.

  5. plugin/skills/cite-encode/SKILL.md

    Not read

    Components using this file 1

    • cite-encode plugin/skills/cite-encode/SKILL.md

    Fields declared in the file

    Compatibility (declared in file)
    Not readNo usable header, which says neither that it was declared nor that it was not.
    License text (declared in file, unverified)
    Not readNo usable header, which says neither that it was declared nor that it was not.
    metadata.version (file annotation)
    Not readNo usable header, which says neither that it was declared nor that it was not.

    This file has no usable extraction record yet, so all three fields show as “Not read”.

    Repository
    ammawla/encode-toolkit
    Pinned commit
    36836c8725fd4d20d9c851ce314f5151aea5f57c
    File identity
    Regular-file identity recorded
    Blob SHA
    d76ccb3d855cc039fc53a6f043c8637685d24ca1
    Mode
    100644
    Identity recorded
    Header parse
    Not read
    Why not read
    The file identity is recorded, but its content has not been read yet. declaration_unread

    No extraction record yet.

  6. plugin/skills/clinvar-annotation/SKILL.md

    Not read

    Components using this file 1

    • clinvar-annotation plugin/skills/clinvar-annotation/SKILL.md

    Fields declared in the file

    Compatibility (declared in file)
    Not readNo usable header, which says neither that it was declared nor that it was not.
    License text (declared in file, unverified)
    Not readNo usable header, which says neither that it was declared nor that it was not.
    metadata.version (file annotation)
    Not readNo usable header, which says neither that it was declared nor that it was not.

    This file has no usable extraction record yet, so all three fields show as “Not read”.

    Repository
    ammawla/encode-toolkit
    Pinned commit
    36836c8725fd4d20d9c851ce314f5151aea5f57c
    File identity
    Regular-file identity recorded
    Blob SHA
    6f1deb01f0e9fd657b0f65e69a2f783360e09ccc
    Mode
    100644
    Identity recorded
    Header parse
    Not read
    Why not read
    The file identity is recorded, but its content has not been read yet. declaration_unread

    No extraction record yet.

  7. plugin/skills/compare-biosamples/SKILL.md

    Not read

    Components using this file 1

    • compare-biosamples plugin/skills/compare-biosamples/SKILL.md

    Fields declared in the file

    Compatibility (declared in file)
    Not readNo usable header, which says neither that it was declared nor that it was not.
    License text (declared in file, unverified)
    Not readNo usable header, which says neither that it was declared nor that it was not.
    metadata.version (file annotation)
    Not readNo usable header, which says neither that it was declared nor that it was not.

    This file has no usable extraction record yet, so all three fields show as “Not read”.

    Repository
    ammawla/encode-toolkit
    Pinned commit
    36836c8725fd4d20d9c851ce314f5151aea5f57c
    File identity
    Regular-file identity recorded
    Blob SHA
    0e85e0c4f8b3f2acbb092d2ddae36be61531ea69
    Mode
    100644
    Identity recorded
    Header parse
    Not read
    Why not read
    The file identity is recorded, but its content has not been read yet. declaration_unread

    No extraction record yet.

  8. plugin/skills/cross-reference/SKILL.md

    Not read

    Components using this file 1

    • cross-reference plugin/skills/cross-reference/SKILL.md

    Fields declared in the file

    Compatibility (declared in file)
    Not readNo usable header, which says neither that it was declared nor that it was not.
    License text (declared in file, unverified)
    Not readNo usable header, which says neither that it was declared nor that it was not.
    metadata.version (file annotation)
    Not readNo usable header, which says neither that it was declared nor that it was not.

    This file has no usable extraction record yet, so all three fields show as “Not read”.

    Repository
    ammawla/encode-toolkit
    Pinned commit
    36836c8725fd4d20d9c851ce314f5151aea5f57c
    File identity
    Regular-file identity recorded
    Blob SHA
    f2944fd2c024547682fb8df9e66e9f3f62afe2a8
    Mode
    100644
    Identity recorded
    Header parse
    Not read
    Why not read
    The file identity is recorded, but its content has not been read yet. declaration_unread

    No extraction record yet.

  9. plugin/skills/data-provenance/SKILL.md

    Not read

    Components using this file 1

    • data-provenance plugin/skills/data-provenance/SKILL.md

    Fields declared in the file

    Compatibility (declared in file)
    Not readNo usable header, which says neither that it was declared nor that it was not.
    License text (declared in file, unverified)
    Not readNo usable header, which says neither that it was declared nor that it was not.
    metadata.version (file annotation)
    Not readNo usable header, which says neither that it was declared nor that it was not.

    This file has no usable extraction record yet, so all three fields show as “Not read”.

    Repository
    ammawla/encode-toolkit
    Pinned commit
    36836c8725fd4d20d9c851ce314f5151aea5f57c
    File identity
    Regular-file identity recorded
    Blob SHA
    716c10751bb3710fb23a3df4432fb94d3e07bb27
    Mode
    100644
    Identity recorded
    Header parse
    Not read
    Why not read
    The file identity is recorded, but its content has not been read yet. declaration_unread

    No extraction record yet.

  10. plugin/skills/disease-research/SKILL.md

    Not read

    Components using this file 1

    • disease-research plugin/skills/disease-research/SKILL.md

    Fields declared in the file

    Compatibility (declared in file)
    Not readNo usable header, which says neither that it was declared nor that it was not.
    License text (declared in file, unverified)
    Not readNo usable header, which says neither that it was declared nor that it was not.
    metadata.version (file annotation)
    Not readNo usable header, which says neither that it was declared nor that it was not.

    This file has no usable extraction record yet, so all three fields show as “Not read”.

    Repository
    ammawla/encode-toolkit
    Pinned commit
    36836c8725fd4d20d9c851ce314f5151aea5f57c
    File identity
    Regular-file identity recorded
    Blob SHA
    df84a3955b89450dd3e3e7aca71a732da988f1d0
    Mode
    100644
    Identity recorded
    Header parse
    Not read
    Why not read
    The file identity is recorded, but its content has not been read yet. declaration_unread

    No extraction record yet.

  11. plugin/skills/download-encode/SKILL.md

    Not read

    Components using this file 1

    • download-encode plugin/skills/download-encode/SKILL.md

    Fields declared in the file

    Compatibility (declared in file)
    Not readNo usable header, which says neither that it was declared nor that it was not.
    License text (declared in file, unverified)
    Not readNo usable header, which says neither that it was declared nor that it was not.
    metadata.version (file annotation)
    Not readNo usable header, which says neither that it was declared nor that it was not.

    This file has no usable extraction record yet, so all three fields show as “Not read”.

    Repository
    ammawla/encode-toolkit
    Pinned commit
    36836c8725fd4d20d9c851ce314f5151aea5f57c
    File identity
    Regular-file identity recorded
    Blob SHA
    ae81744b2a8aff3bd366ca1daaecf023e7ddd971
    Mode
    100644
    Identity recorded
    Header parse
    Not read
    Why not read
    The file identity is recorded, but its content has not been read yet. declaration_unread

    No extraction record yet.

  12. plugin/skills/ensembl-annotation/SKILL.md

    Not read

    Components using this file 1

    • ensembl-annotation plugin/skills/ensembl-annotation/SKILL.md

    Fields declared in the file

    Compatibility (declared in file)
    Not readNo usable header, which says neither that it was declared nor that it was not.
    License text (declared in file, unverified)
    Not readNo usable header, which says neither that it was declared nor that it was not.
    metadata.version (file annotation)
    Not readNo usable header, which says neither that it was declared nor that it was not.

    This file has no usable extraction record yet, so all three fields show as “Not read”.

    Repository
    ammawla/encode-toolkit
    Pinned commit
    36836c8725fd4d20d9c851ce314f5151aea5f57c
    File identity
    Regular-file identity recorded
    Blob SHA
    3e2c3a54e993ca266ab6ed4ddfa9e204c128b58e
    Mode
    100644
    Identity recorded
    Header parse
    Not read
    Why not read
    The file identity is recorded, but its content has not been read yet. declaration_unread

    No extraction record yet.

  13. plugin/skills/epigenome-profiling/SKILL.md

    Not read

    Components using this file 1

    • epigenome-profiling plugin/skills/epigenome-profiling/SKILL.md

    Fields declared in the file

    Compatibility (declared in file)
    Not readNo usable header, which says neither that it was declared nor that it was not.
    License text (declared in file, unverified)
    Not readNo usable header, which says neither that it was declared nor that it was not.
    metadata.version (file annotation)
    Not readNo usable header, which says neither that it was declared nor that it was not.

    This file has no usable extraction record yet, so all three fields show as “Not read”.

    Repository
    ammawla/encode-toolkit
    Pinned commit
    36836c8725fd4d20d9c851ce314f5151aea5f57c
    File identity
    Regular-file identity recorded
    Blob SHA
    170cabf64283c9f24f694f554a668c9484c030c5
    Mode
    100644
    Identity recorded
    Header parse
    Not read
    Why not read
    The file identity is recorded, but its content has not been read yet. declaration_unread

    No extraction record yet.

  14. plugin/skills/functional-screen-analysis/SKILL.md

    Not read

    Components using this file 1

    • functional-screen-analysis plugin/skills/functional-screen-analysis/SKILL.md

    Fields declared in the file

    Compatibility (declared in file)
    Not readNo usable header, which says neither that it was declared nor that it was not.
    License text (declared in file, unverified)
    Not readNo usable header, which says neither that it was declared nor that it was not.
    metadata.version (file annotation)
    Not readNo usable header, which says neither that it was declared nor that it was not.

    This file has no usable extraction record yet, so all three fields show as “Not read”.

    Repository
    ammawla/encode-toolkit
    Pinned commit
    36836c8725fd4d20d9c851ce314f5151aea5f57c
    File identity
    Regular-file identity recorded
    Blob SHA
    37889f1e2a7dfc749dce72723faeb36d2b773f5b
    Mode
    100644
    Identity recorded
    Header parse
    Not read
    Why not read
    The file identity is recorded, but its content has not been read yet. declaration_unread

    No extraction record yet.

  15. plugin/skills/geo-connector/SKILL.md

    Not read

    Components using this file 1

    • geo-connector plugin/skills/geo-connector/SKILL.md

    Fields declared in the file

    Compatibility (declared in file)
    Not readNo usable header, which says neither that it was declared nor that it was not.
    License text (declared in file, unverified)
    Not readNo usable header, which says neither that it was declared nor that it was not.
    metadata.version (file annotation)
    Not readNo usable header, which says neither that it was declared nor that it was not.

    This file has no usable extraction record yet, so all three fields show as “Not read”.

    Repository
    ammawla/encode-toolkit
    Pinned commit
    36836c8725fd4d20d9c851ce314f5151aea5f57c
    File identity
    Regular-file identity recorded
    Blob SHA
    8106b25241b1501b6404e6b58f9446eedab11e87
    Mode
    100644
    Identity recorded
    Header parse
    Not read
    Why not read
    The file identity is recorded, but its content has not been read yet. declaration_unread

    No extraction record yet.

  16. plugin/skills/gnomad-variants/SKILL.md

    Not read

    Components using this file 1

    • gnomad-variants plugin/skills/gnomad-variants/SKILL.md

    Fields declared in the file

    Compatibility (declared in file)
    Not readNo usable header, which says neither that it was declared nor that it was not.
    License text (declared in file, unverified)
    Not readNo usable header, which says neither that it was declared nor that it was not.
    metadata.version (file annotation)
    Not readNo usable header, which says neither that it was declared nor that it was not.

    This file has no usable extraction record yet, so all three fields show as “Not read”.

    Repository
    ammawla/encode-toolkit
    Pinned commit
    36836c8725fd4d20d9c851ce314f5151aea5f57c
    File identity
    Regular-file identity recorded
    Blob SHA
    9c880bcb39f624251231e2b25cdc3cfd816d2a10
    Mode
    100644
    Identity recorded
    Header parse
    Not read
    Why not read
    The file identity is recorded, but its content has not been read yet. declaration_unread

    No extraction record yet.

  17. plugin/skills/gtex-expression/SKILL.md

    Not read

    Components using this file 1

    • gtex-expression plugin/skills/gtex-expression/SKILL.md

    Fields declared in the file

    Compatibility (declared in file)
    Not readNo usable header, which says neither that it was declared nor that it was not.
    License text (declared in file, unverified)
    Not readNo usable header, which says neither that it was declared nor that it was not.
    metadata.version (file annotation)
    Not readNo usable header, which says neither that it was declared nor that it was not.

    This file has no usable extraction record yet, so all three fields show as “Not read”.

    Repository
    ammawla/encode-toolkit
    Pinned commit
    36836c8725fd4d20d9c851ce314f5151aea5f57c
    File identity
    Regular-file identity recorded
    Blob SHA
    951c8ce617c3a8508223e889430b591e38ff3575
    Mode
    100644
    Identity recorded
    Header parse
    Not read
    Why not read
    The file identity is recorded, but its content has not been read yet. declaration_unread

    No extraction record yet.

  18. plugin/skills/gwas-catalog/SKILL.md

    Not read

    Components using this file 1

    • gwas-catalog plugin/skills/gwas-catalog/SKILL.md

    Fields declared in the file

    Compatibility (declared in file)
    Not readNo usable header, which says neither that it was declared nor that it was not.
    License text (declared in file, unverified)
    Not readNo usable header, which says neither that it was declared nor that it was not.
    metadata.version (file annotation)
    Not readNo usable header, which says neither that it was declared nor that it was not.

    This file has no usable extraction record yet, so all three fields show as “Not read”.

    Repository
    ammawla/encode-toolkit
    Pinned commit
    36836c8725fd4d20d9c851ce314f5151aea5f57c
    File identity
    Regular-file identity recorded
    Blob SHA
    4d0f6939bd749f8e99f3917b8ee47a96edb61461
    Mode
    100644
    Identity recorded
    Header parse
    Not read
    Why not read
    The file identity is recorded, but its content has not been read yet. declaration_unread

    No extraction record yet.

  19. plugin/skills/hic-aggregation/SKILL.md

    Not read

    Components using this file 1

    • hic-aggregation plugin/skills/hic-aggregation/SKILL.md

    Fields declared in the file

    Compatibility (declared in file)
    Not readNo usable header, which says neither that it was declared nor that it was not.
    License text (declared in file, unverified)
    Not readNo usable header, which says neither that it was declared nor that it was not.
    metadata.version (file annotation)
    Not readNo usable header, which says neither that it was declared nor that it was not.

    This file has no usable extraction record yet, so all three fields show as “Not read”.

    Repository
    ammawla/encode-toolkit
    Pinned commit
    36836c8725fd4d20d9c851ce314f5151aea5f57c
    File identity
    Regular-file identity recorded
    Blob SHA
    5a925138f44fc6e51e49a94f8eda5a4a5102f2a3
    Mode
    100644
    Identity recorded
    Header parse
    Not read
    Why not read
    The file identity is recorded, but its content has not been read yet. declaration_unread

    No extraction record yet.

  20. plugin/skills/histone-aggregation/SKILL.md

    Not read

    Components using this file 1

    • histone-aggregation plugin/skills/histone-aggregation/SKILL.md

    Fields declared in the file

    Compatibility (declared in file)
    Not readNo usable header, which says neither that it was declared nor that it was not.
    License text (declared in file, unverified)
    Not readNo usable header, which says neither that it was declared nor that it was not.
    metadata.version (file annotation)
    Not readNo usable header, which says neither that it was declared nor that it was not.

    This file has no usable extraction record yet, so all three fields show as “Not read”.

    Repository
    ammawla/encode-toolkit
    Pinned commit
    36836c8725fd4d20d9c851ce314f5151aea5f57c
    File identity
    Regular-file identity recorded
    Blob SHA
    abcde7d757cd812e19faf7291494481d06768287
    Mode
    100644
    Identity recorded
    Header parse
    Not read
    Why not read
    The file identity is recorded, but its content has not been read yet. declaration_unread

    No extraction record yet.

Read this page as JSON

All versions1

Each commit is an immutable snapshot, newest first. One version label can map to several commits.

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0.3.4 Latest 36836c8 65 View Download Compare…