scikit-bio-tutorials

Interactive tutorials for using scikit-bio in biological research.

This repository hosts tutorial materials for the ISMB 2024 conference.

• https://www.iscb.org/ismb2024/programme-schedule/tutorials#ip3

The tutorial is broken down as follows, Google Colab notebooks can be launched via the following links

1. Section 01: Basic bioinformatics using scikit-bio
2. Section 02: Embeddings and Vectors with Scikit-Bio
3. Section 03: Working with various omic data types
4. Section 04: Analyzing microbial communities
5. Section 05: Comparing microbial community structure
6. Section 06: Inferring and associating critical features
7. Section 07: Predicting host and environmental traits

The example dataset(s) are available for download at Dropbox:

• https://www.dropbox.com/scl/fo/euir18o3jb4pglljaxslo/AKNF1Lk3sQ52ZTn_A-z2sqc?rlkey=u72814al272kvu17rnozsr5jp&dl=0

Alternatively, the tutorial materials (notebooks, slides, and datasets) are shared at Google Drive:

• https://drive.google.com/drive/folders/1YSpEBHrGM_fjmiN5NpwdgLL3WtT0VTsy?usp=sharing

References

1. Protein remote homology detection and structural alignment using deep learning
2. ProtTrans: Towards Cracking the Language of Life’s Code Through Self-Supervised Learning
3. UniFrac: a New Phylogenetic Method for Comparing Microbial Communities
4. Establishing microbial composition measurement standards with reference frames
5. Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis
6. Balances: a New Perspective for Microbiome Analysis
7. Compositionally Aware Phylogenetic Beta-Diversity Measures Better Resolve Microbiomes Associated with Phenotype