A single cell RNA-seq downstream analysis pipeline that performs QC filtering, normalization, highly variable gene selection, PCA, UMAP embedding, and Leiden clustering. Takes raw count h5ad files as input and produces UMAP plots, QC plots, and processed h5ad files.

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.

Bulk RNA-seq preprocessing pipeline using nf-core/rnaseq v3.22.2 with the STAR-Salmon workflow. Takes raw paired-end FASTQ files, performs quality control (FastQC, TrimGalore), alignment (STAR), quantification (Salmon), and generates a comprehensive MultiQC report. iGenomes is disabled by default; users provide their own reference FASTA and GTF files.

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.