https://github.com/maayanlab/maayanlab-bioinformatics
A collection of useful functions for bioinformatics data analysis
https://github.com/maayanlab/maayanlab-bioinformatics
Last synced: 7 months ago
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A collection of useful functions for bioinformatics data analysis
- Host: GitHub
- URL: https://github.com/maayanlab/maayanlab-bioinformatics
- Owner: MaayanLab
- License: apache-2.0
- Created: 2020-05-21T16:57:11.000Z (over 5 years ago)
- Default Branch: master
- Last Pushed: 2025-06-04T15:53:49.000Z (8 months ago)
- Last Synced: 2025-06-04T21:49:32.608Z (8 months ago)
- Language: Python
- Homepage: https://maayanlab.github.io/maayanlab-bioinformatics/
- Size: 5.5 MB
- Stars: 23
- Watchers: 4
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Ma'ayanlab Bioinformatics
A collection of useful functions for bioinformatics data analysis.
This library contains many functions and methods I use again and again in different analyses including:
- quantile normalization
- other common normalizations
- logcpm, zscore, filter variance
- gmt parser
- single-cell sparse matrix parsing
- transcript to gene conversions
- ...
- various dge including chdir, lima_voom, deseq2, etc..
## Installation
```
# minimal
pip install "maayanlab-bioinformatics@git+https://github.com/Maayanlab/maayanlab-bioinformatics.git"
# complete
pip install "maayanlab-bioinformatics[all]@git+https://github.com/Maayanlab/maayanlab-bioinformatics.git"
# [OPTIONAL] for some R functionality like limma_voom & filter_by_expr
python -m maayanlab_bioinformatics.setup.R
```