Notebooks

Runnable Jupyter notebooks that walk through the Python API. They are rendered as static HTML here; click any notebook to download or run it yourself.

Notebook map

BAM.ipynb

Read a BAM file, compute alignment statistics, plot insert size.

coverage.ipynb

Companion to Library user guide — running median + z-score on a BED.

fastq_module.ipynb

Iterate over FastQ records, filter and re-write.

featurecounts.ipynb

Load a featureCounts table, inspect the count matrix.

ribodesigner.ipynb

Design ribosomal-depletion probes from a FASTA + GFF.