genomic-features

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`cookiecutter-scverse` released [v0.4.0](https://github.com/scverse/cookiecutter-scverse/releases/tag/v0.4.0). ## Changes ## What's Changed * pre-commit updates * Fix installation instructions on contributing guide by @grst in https://github.com/scverse/cookiecutter-scverse/pull/271 * fix typo by @Zethson in https://github.com/scverse/cookiecutter-scverse/pull/279 *...

scverse-bot

updates: - [github.com/astral-sh/ruff-pre-commit: v0.3.7 → v0.14.6](https://github.com/astral-sh/ruff-pre-commit/compare/v0.3.7...v0.14.6) - [github.com/pre-commit/pre-commit-hooks: v4.6.0 → v6.0.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.6.0...v6.0.0) - [github.com/codespell-project/codespell: v2.2.6 → v2.4.1](https://github.com/codespell-project/codespell/compare/v2.2.6...v2.4.1)

pre-commit-ci[bot]

Add UCSC TxDb

3

Work for issue #11 This is currently a very dirty WIP, the doc is missing, the notebook is in the wrong place and will be turned into a cookbook

gamazeps

Sort output

4

This PR orders the results. By default, it's ordered by chrom, start, and id. Custom ordering can be provided using `order_by`. If subsets of columns are selected, then the columns...

thomas-reimonn

Example where we directly connect to the ensembl servers

1

### Description of feature It would be nice to have an example where we directly connect to the ensembl mysql servers to run a query. Especially for the biomart version,...

ivirshup

Better downloads

1

### Description of feature Currently we grab data from bioconductor's AnnotationHub. This is very convenient, but we're grabbing uncompressed sqlite files. When bioc distributes these files as packages, they are...

ivirshup

Conversion of seqlevel styles

2

### Description of feature Add functionality that allows translation between different chromosome sequence naming conventions (e.g., "chr1" versus "1"). This could be similar to the `seqlevelsStyle` function in the [R...

lauradmartens

Defining the main genomic coordinates for each table

2

### Description of feature For each table available via EnsemblDb (e.g. `genes`, `promoters`) we could rename the primary genomic coordinates to the format required by `bioframe` (e.g. `chrom`, `start`, `end`)....

emdann

User guide section: filters

1

### Description of feature It would be good to have a user guide section with a brief explanation of how filters can be combined.

ivirshup

What order should results be in?

7

### Description of feature Continuing from https://github.com/scverse/genomic-features/pull/59#issuecomment-2034149437 In the mentioned PR, we found out that duckdb is inconsistent with what order it returns results in. This by and large seems...

ivirshup