Comments (6)
I think it is really important for future users that the usage guide works without errors. Otherwise, the user might get frustrated and refrains from using the library. So the usage guide should be updated according to the functionalities and current version of the package. But I think this can also happen while the package is further developed.
from openomics.
An overview of all methods and functions of the package would be helpful.
from openomics.
'OpenOmics facilitates the common coding tasks when preparing data for bioinformatics analysis.': For which bioinformatic analyses exactly?
The statement of need was written to be more general since I intended openomics to handle data wrangling tasks for any bioinformatics analysis that involve tabular-structured data. I just edited the package description on the readme.md
to be a little more specific:
This Python package provide a series of tools to integrate and query the genomics, transcriptomics, proteomics, and
clinical data (aka multi-omics data). With scalable data-frame manipulation tools, OpenOmics facilitates the common
data wrangling tasks when preparing data for RNA-seq bioinformatics analysis.
What are specific usage examples (also e.g. after using OpenOmics: What's next?)
For now, OpenOmics's data wrangling operations are meant to be agnostic on any particular bioinformatics analysis. After using OpenOmics for data exploration, the user would be free to do any kind of analysis on the processed data. But I can write more usage guides on RTD for different examples of down-stream analyses, such as saving to files, visualizations, etc.
An overview of all methods and functions of the package would be helpful.
On the RTD documentations, I've compiled the API Reference sections for browsing the classes and functions for various submodules in openomics. Although I haven't written a guide on the overview of different classes or docstrings for every modules and functions yet, I think this directory (and the likes) should give an overview over all the submodules of the package.
from openomics.
Thank you for your quick reply!
I definitely like the package description and the documentations better now. The usage examples are good the way they are now. So these comments are all addressed in my opinion!
There is still one more issue with the tutorial 'Preparing data for downstream analyses':
To prepare the data for classification
# This function selects only patients with patholotic stages "Stage I" and "Stage II"
X_multiomics, y = luad_data.load_dataframe(,,
SyntaxError: invalid syntax (, line 1)
from openomics.
Hi @ksielemann thanks for pointing this out. I've just fixed the vignette at https://openomics.readthedocs.io/en/latest/usage/preprocess-downstream-analysis.html#to-prepare-the-data-for-classification
Honestly this usage guide (and a few others) do need an update since a lot of the underlying functionalities has been changed since they were written. I also have plan to add more key functionalities in the near future, so the guides will be rudimentary until those features have been implemented.
from openomics.
Yes, I agree with that wholeheartedly. Will try my best to update them!
from openomics.
Related Issues (13)
- AttributeError: '_io.TextIOWrapper' object has no attribute 'startswith' HOT 7
- Reviewer 1 - comment 2 - Cannot change the directory of downloaded Dataset files (using astropy) HOT 2
- Reviewer 2 - Installation instructions - Unable to install dependency HOT 2
- Reviewer 2 - Vignette - Unable to `import umap` due to dependencies with scipy on Python 3.9 HOT 2
- Reviewer 2 - Automated tests - Errors with importing dataset in generate_MiRTarBase test HOT 3
- Review 2 - Automated tests - Failed builds in Travis CI HOT 10
- Review 2 - Documentations - Readthedocs documentations should be updated HOT 4
- Reviewer 1 - errors using the example code HOT 1
- Reviewer 1 - Installation HOT 2
- Unable to use load_data() for class Multiomics HOT 4
- Test Suite Errors HOT 1
- Initial Update
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