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1. germline-variant-calling-pipeline germline-variant-calling-pipeline Public

   A workflow for germline variant calling from raw sequencing data. Covers quality control, alignment, variant calling, filtering, and annotation.

   Python

2. RNASeq-Analysis-Pipeline RNASeq-Analysis-Pipeline Public

   A complete RNA-Seq analysis workflow, from raw FASTQ files to Differential Gene Expression (DGE) analysis. Includes quality control, read alignment, quantification, normalization, statistical testi…

   R

3. scRNA-seq-Seurat-Workflow scRNA-seq-Seurat-Workflow Public

   A modular and reproducible Snakemake workflow for single-cell RNA-seq analysis using the Seurat R package. This pipeline processes 10x Genomics PBMC3k data from quality control through clustering a…

   R 1

4. somatic-variant-calling-pipeline somatic-variant-calling-pipeline Public

   A workflow for somatic variant calling in tumor-normal paired samples. Includes quality control, alignment, variant detection, filtering, annotation, and downstream analysis.

   Python

5. rnaseq-atacseq-integration-workflow rnaseq-atacseq-integration-workflow Public

   This Snakemake-based workflow provides a modular and reproducible pipeline for processing and integrating bulk RNA-seq and ATAC-seq datasets. It covers raw data preprocessing, quality control, alig…

   Python 1 1

6. GermlineSNPs-NF GermlineSNPs-NF Public

   Nextflow pipeline for germline SNP analysis using BWA, GATK, and SnpEff in a Singularity container.

   Nextflow