Self-contained demonstrations of sequencing analysis and lab automation. Each demo generates synthetic data, plants known ground truth, runs one method, and scores the result.
The repository contains no proprietary data or code.
pip install -r requirements.txt
make all
# Run one demo
make methylation
make scrna-umi
make scrna-cell-calling
make rna
make demux
make variant
make cnv
make pcr-enrichment
make chromatinPython 3.10 or newer is recommended. PyLabRobot is used only by the PCR-enrichment automation demo, and SciPy is used only by the bulk RNA-seq demo.
Conversion efficiency, CpG protection, coverage, and global methylation across standard and low-input synthetic libraries.
Open the methylation-sequencing demo
Directional and adjacency-based UMI collapse recover molecule counts from duplicated, error-containing synthetic scRNA-seq reads.
Max-curvature knee calling separates cells from ambient barcodes in a synthetic multiplexed, probe-based scRNA-seq count matrix.
Open the scRNA-seq cell-calling demo
CPM normalization, PCA, Welch's t-test, and false-discovery-rate correction on a two-condition count matrix.
Exact i7/i5 pair assignment and synthetic index-hopping measurement.
Synthetic pileup, allele-fraction thresholding, and SNV precision/recall scoring.
GC-corrected coverage, rolling-median segmentation, and gain/loss calling.
PCR enrichment, SPRI cleanup, and indexing on a simulated liquid handler through PyLabRobot. The executed transfers and exported worklist share one source plan.
Open the PCR-enrichment automation demo
An interactive CUT&Tag track browser over a synthetic locus with threshold-based peak calling.
Open the chromatin-browser demo
MIT; see LICENSE.