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Update updates.md
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lauraluebbert committed Feb 9, 2024
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- Allow missing gene filter for [`gget cellxgene`](cellxgene.md) (fixes [bug](https://github.com/pachterlab/gget/issues/110))
- [`gget seq`](./seq.md): Allow missing gene names (fixes [https://github.com/pachterlab/gget/issues/107](https://github.com/pachterlab/gget/issues/107))
- **[`gget enrichr`](enrichr.md): Use new arguments `kegg_out` and `kegg_rank` to create an image of the KEGG pathway with the genes from the enrichment analysis highlighted (thanks to [this PR](https://github.com/pachterlab/gget/pull/106) by [Noriaki Sato](https://github.com/noriakis))**
- New modules: [`gget elm`](elm.md) and [`gget diamond`](diamond.md)
- **New modules: [`gget elm`](elm.md) and [`gget diamond`](diamond.md)**

**Version ≥ 0.27.9** (August 7, 2023):
- **[`gget enrichr`](enrichr.md): Use new argument `background_list` to provide a list of background genes**
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- Added `census_version` argument to [`gget cellxgene`](cellxgene.md).

**Version ≥ 0.27.6** (May 1, 2023) (YANKED due to problems with dependencies -> replaced with version 0.27.7):
**- Thanks to PR by [Tomás Di Domenico](https://github.com/tdido): [`gget search`](search.md) can now also query plant 🌱 Ensembl IDs. **
- New module: [`gget cellxgene`](cellxgene.md)
- **Thanks to PR by [Tomás Di Domenico](https://github.com/tdido): [`gget search`](search.md) can now also query plant 🌱 Ensembl IDs.**
- **New module: [`gget cellxgene`](cellxgene.md)**

**Version ≥ 0.27.5** (April 6, 2023):
- Updated [`gget search`](search.md) to function correctly with new [Pandas](https://pypi.org/project/pandas/2.0.0/) version 2.0.0 (released on April 3rd, 2023) as well as older versions of Pandas
- Updated [`gget info`](info.md) with new flags `uniprot` and `ncbi` which allow turning off results from these databases independently to save runtime (note: flag `ensembl_only` was deprecated)
- All gget modules now feature a `-q / --quiet` (Python: `verbose=False`) flag to turn off progress information

**Version ≥ 0.27.4** (March 19, 2023):
- New module: [`gget gpt`](gpt.md)

- **New module: [`gget gpt`](gpt.md)**
**Version ≥ 0.27.3** (March 11, 2023):
- [`gget info`](info.md) excludes PDB IDs by default to increase speed (PDB results can be included using flag `--pdb` / `pdb=True`).

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- Reduced runtime for [`gget info`](info.md) and [`gget seq`](seq.md)

**Version ≥ 0.3.11** (September 7, 2022):
- New module: [`gget pdb`](pdb.md)
- **New module: [`gget pdb`](pdb.md)**

**Version ≥ 0.3.10** (September 2, 2022):
- [`gget alphafold`](alphafold.md) now also returns pLDDT values for generating plots from output without rerunning the program (also see the [gget alphafold FAQ](https://github.com/pachterlab/gget/discussions/39))
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- **NOTE:** The [Ensembl FTP site](http://ftp.ensembl.org/pub/) changed its structure on August 8, 2022. Please upgrade to `gget` version ≥ 0.3.7 if you use [`gget ref`](ref.md)

**Version ≥ 0.3.5** (August 6, 2022):
- New module: [`gget alphafold`](alphafold.md)
- **New module: [`gget alphafold`](alphafold.md)**

**Version ≥ 0.2.6** (July 7, 2022):
- [`gget ref`](ref.md) now supports plant genomes! 🌱
- **[`gget ref`](ref.md) now supports plant genomes! 🌱**

**Version ≥ 0.2.5** (June 30, 2022):
- **NOTE:** [UniProt](https://www.uniprot.org/) changed the structure of their API on June 28, 2022. Please upgrade to `gget` version ≥ 0.2.5 if you use any of the modules querying data from UniProt ([`gget info`](info.md) and [`gget seq`](seq.md)).
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