Multi-sample somatic variant caller
RNAseq pipeline for alternative splicing junctions
Fast, epiallele-aware methylation caller and reporter — an R/Bioconductor package
An end-to-end RNA-seq pipeline for gene expression analysis and differential expression using FASTQ data, Bowtie2, SAMtools, and R (DESeq2, Gviz, etc.).
Obtaining case-associated variants and correspondent genes (from control/case experiments) in BASH/R enviroment
Sequencing data preprocessing
A reproducible RNA-Seq analysis pipeline for Staphylococcus aureus under antibiotic stress, utilizing Nextflow and Singularity. It involves genome mapping, read counting, and statistical analysis to identify differentially expressed genes (DEGs) and generates key visualizations.
A streamlined pipeline for germline variant calling on chromosome 11 using GATK. This repository includes workflows for data preprocessing, variant discovery, and annotation, with a focus on understanding genetic variations linked to disease-associated genes.
Repository for bulk RNA-seq analyses (from undergrad 2nd-3rd year) – Reorganized
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