Scanpy-based single-cell RNA-seq analysis pipeline for mouse scRNA-seq data. Includes QC, normalization, HVG selection, PCA, Leiden clustering, and UMAP visualization.

Bulk RNA-seq preprocessing pipeline that wraps nf-core/rnaseq (v3.22.2) with the STAR-Salmon workflow. Takes raw FASTQ files and a samplesheet as input, performs quality control, trimming, alignment with STAR, quantification with Salmon, and produces a comprehensive MultiQC report along with gene/transcript-level count matrices.

AptaSelect identifies high-frequency aptamer candidate sequences from paired-end FASTQ files produced by SELEX experiments. The pipeline joins paired-end reads, applies three sequential pattern-based filtering stages (Selection, 1st Sort, 2nd Sort), and aggregates and ranks sequences by frequency at each stage.

Variant-aware Cas-OFFinder pipeline (version 2) that identifies potential CRISPR off-target sites accounting for individual genetic variants. The pipeline normalizes a phased single-sample VCF using vcfallelicprimitives, bcftools norm, and vcfcreatemulti, splits by chromosome to avoid segfaults, generates allelic FASTA files with vcf2fasta, and runs cas-offinder per individual FASTA file.

A Snakemake pipeline that performs differential expression analysis on Salmon-quantified Bulk RNA-seq data using edgeR (TMM/quasi-likelihood), followed by downstream functional enrichment analyses including GO over-representation, GSEA, Reactome pathway analysis, and Hallmark gene-set scoring. Outputs include DEG Excel tables, volcano plots, and enrichment plots.

A comprehensive 10X Genomics snMultiome (joint snRNA-seq + scATAC-seq) analysis pipeline for reproducing the results from 'Epithelial WNT secretion drives niche escape of developing gastric cancer'. The pipeline processes wild-type (RZ) and KRAS-mutant (RZK) mouse gastric tissue samples through QC filtering, MACS2 peak calling, SCTransform + TF-IDF normalisation, SCT-based integration, UMAP clustering, differential expression (MAST), differential accessibility (LR test), KRAS signaling gene set overlap, and JASPAR2020 TF motif enrichment analysis. Generates publication-quality figures including UMAP plots, DotPlots, dittoBarPlots, FeaturePlots, and motif enrichment bar plots.

Data-driven signal detection for unbiased scRNA-seq data analysis using scLENS (Single-cell Low-dimension Embedding using effective Noise Subtraction). Performs QC, dimensionality reduction via RMT-based noise filtering, and UMAP visualization.

End-to-end variant calling pipeline from paired-end FASTQ reads using Octopus, a haplotype-aware Bayesian variant caller. Includes quality control (FastQC), adapter trimming (fastp), read alignment (BWA-MEM2), haplotype-based variant detection (Octopus), and quality filtering (bcftools). Detects SNPs, indels, and complex variants using particle filtering.

End-to-end variant calling pipeline from paired-end FASTQ reads using freebayes. Includes quality control (FastQC), adapter trimming (fastp), read alignment (BWA-MEM2), Bayesian variant detection (freebayes), and quality filtering (bcftools). Produces filtered VCF with SNPs, indels, and MNPs.

Cell segmentation-free spatial cell-type inference using SSAM (Spot-based Spatial cell-type Analysis by Multidimensional mRNA density estimation). Applies KDE to single-molecule mRNA coordinates and maps pixel-level gene expression vectors to cell-type signatures, producing a spatial cell-type map and abundance statistics.