Improve documentation for gene biotype related functions

README.md

@@ -8,7 +8,8 @@
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@@ -96,10 +97,6 @@ Command options are:
 - `-ow`: Provide this flag to overwrite an existing file at the output path.
 - `--help`: Display all configuration options.
 
-## Development status
-
-`pytximport` is still in development and has not yet reached version 1.0.0 in the [SemVer](https://semver.org/) versioning scheme. While it should work for almost all use cases and we regularly compare outputs against the R implementation, breaking changes between minor versions may occur. If you encounter any problems, please open a GitHub issue. If you are a Python developer, we welcome pull requests implementing missing features, adding more extensive unit tests and bug fixes.
-
 ## Motivation
 
 The `tximport` package has become a main stay in the bulk RNA sequencing community and has been used in hundreds of scientific publications. However, its accessibility has remained limited since it requires the R programming language and cannot be used from within Python scripts or the command line. Other tools of the bulk RNA sequencing analysis stack, like `DESeq2` (in the form of `PyDESeq2`), `decoupler`, `liana` and others all have Python versions. Additionally, pseudoalignment tools like `salmon` and `kallisto` can be installed via `conda` and can be used from the command line.
@@ -129,7 +126,7 @@ Features unique to `pytximport`:
 - `SummarizedExperiment`-support to represent outputs in familiar Bioconductor data structures available through the [BiocPy](https://github.com/biocpy) ecosystem.
 - Saving outputs directly to file (use the `output_path` argument).
 - Removing transcript versions from **both** the quantification files and the transcript-to-gene map when `ignore_transcript_version` is provided.
-- Post-hoc biotype-filtering. Set `biotype_filter` to a whitelist of possible biotypes contained within the bar-separated values of your transcript ids.
+- Post-hoc biotype-filtering using `pytximport.utils.filter_by_biotype`.
 
 Features unique to `tximport`:
 - Alevin single-cell RNA-seq data support
@@ -168,6 +165,10 @@ make coverage-report
 The documentation can be build locally by navigating to the `docs` folder and running: `make html`.
 This requires that the development requirements of the package as well as the package itself have been installed in the same virtual environment and that `pandoc` has been added, e.g. by running `brew install pandoc` on macOS operating systems.
 
+## Development status
+
+`pytximport` is still in development and has not yet reached version 1.0.0 in the [SemVer](https://semver.org/) versioning scheme. While it should work for almost all use cases and we regularly compare outputs against the R implementation, breaking changes between minor versions may occur. If you encounter any problems, please open a GitHub issue. If you are a Python developer, we welcome pull requests implementing missing features, adding more extensive unit tests and bug fixes.
+
 ## Data sources
 
 The quantification files used for the unit tests are partly adopted from [tximportData](https://doi.org/doi:10.18129/B9.bioc.tximportData) which in turn used a subsample of the GEUVADIS data: