Research resouces
Bioinformatics pipelines
github.com/dremellab
[High-throughput Alignment and RNA Output Level Detection]
Modular RNA-seq quantification pipeline, designed for seamless integration with downstream analysis tools such as DiffEx
Automates the process from raw FASTQ files to normalized count matrices and interactive reports that use MultiQC for visualization and quality control summaries; these outputs can then be parsed by the DiffEx package to generate additional Quarto-based interactive reports for differential gene expression and gene set enrichment analysis
Supports custom reference generation, making it ideal for virus-host transcriptomic studies
documentation at: https://github.com/dremellab/HAROLD/blob/main/docs/index.md
[Differential Expression Analysis]
Differential gene expression (DGE) analysis tool using edgeR, DESeq2, and limma
Generates interactive DEG and pathways analysis reports
documentation at: https://github.com/dremellab/DiffEx/blob/main/README.md
[Chroma]
forgive the mess, pipeline improvements and feature add-ons are still a work in progress
Input data: ATAC-Seq data
Designed to be versatile and facilitate analysis of data from multi-organism (infected) samples
Can be used with spike-in controls & paired “control” samples