Results for “nf-core-sarek”

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).

Optimize Entity Framework Core queries by fixing N+1 problems, choosing correct tracking modes, using compiled queries, and avoiding common performance traps.

Build video analytics pipelines using NVIDIA DeepStream SDK 9.0 with Python pyservicemaker API, including GStreamer-based video processing, TensorRT inference integration, object detection/tracking, and Kafka/message broker integration.

Build, run, and debug Nextflow data pipelines and nf-core workflows end to end, covering processes, channels, operators, configuration, testing, and deployment to HPC or cloud.

Store and process large N-dimensional arrays with chunking, compression, and parallel I/O, integrating with NumPy, Dask, and Xarray for cloud-native scientific computing.

Scales pandas/NumPy workflows beyond memory with Dask distributed computing — parallel DataFrames, arrays, delayed task graphs, and cluster execution. Use when existing pandas/NumPy code must run on larger-than-RAM data or across clusters, for parallel file processing, distributed ML, or integration with existing pandas code. For out-of-core analytics on a single machine prefer vaex; for in-memory speed prefer polars. Part of the AlterLab Academic Skills suite.

Orchestrates a complete bulk RNA-seq differential-expression study from raw FASTQ reads through QC, alignment, quantification, differential expression, pathway enrichment, and publication figures.

Track investment theses across their lifecycle — from screening idea to closed position with postmortem. Register theses from screener outputs, manage state transitions, attach position sizing, review due dates, and generate postmortem reports with P&L and MAE/MFE analysis.

Guides analysis of Neuropixels recordings from raw data to curated units, covering preprocessing, motion correction, spike sorting, quality metrics, and export.