Results for “pysam”

Read, write, and manipulate genomic datasets including SAM/BAM/CRAM alignments, VCF/BCF variants, and FASTA/FASTQ sequences using a Pythonic interface to htslib.

Run computational fluid dynamics simulations using Python, including Navier-Stokes equations, shallow water, and stratified flows with pseudospectral methods and HPC support.

Read, write, and modify DICOM medical imaging files, including pixel data extraction, anonymization, format conversion, and compression handling.

Read, write, and manipulate DICOM medical imaging files, including pixel data extraction, metadata editing, anonymization, format conversion, and compression handling.

Build, fit, validate, and compare Bayesian models using PyMC's modern API, including hierarchical models, MCMC sampling, variational inference, posterior predictive checks, and model comparison.

Implement Python database access with parameterized SQL, transaction scope, connection helpers, and repository seams. Use when editing Postgres queries, repositories, transactions, pooling, or persistence boundaries in Python.

Write, review, debug, test, and optimize Python Polars code with version-grounded object types, schemas, and execution boundaries.

Write, review, debug, test, or optimize Python code using PyArrow arrays, schemas, tables, compute kernels, datasets, Parquet, and Arrow IPC.

SQLAlchemy Python SQL toolkit and ORM with powerful query builder, relationship mapping, and database migrations via Alembic

Validates inputs, generates samplesheets and launch scripts, and optionally executes nf-core/pacsomatic matched tumor-normal workflows from BAM files, supporting local runs and scheduler submission (LSF/Slurm/PBS/SGE).