Aggregate results from bioinformatics analyses across many samples into a single report.
TaxTriage is a Nextflow workflow designed to agnostically identify and give confidences of microbial organisms within short- or long-read metagenomic NGS data. This flexible tool was developed with various use-cases of mNGS in mind.
Test data for MultiQC.
A simple fastp-MultiQC nextflow pipeline
RNA-seq analysis from FASTQ to biology: STAR alignment, gene-level counts, DESeq2 differential expression, and GO/KEGG/GSEA. Metadata-driven design with human/mouse/rat support.
AlphaFold-based Protein Analysis Pipeline
ChIP-seq analysis: QC and contamination screening, Bowtie2 alignment, MACS2 broad peaks, DiffBind, and monaLisa/JASPAR motif enrichment, with a MultiQC report.
ORACLE bulk ATAC-seq pipeline (Snakemake + conda): FASTQ/SRA to differential chromatin accessibility, peak annotation, TF motif enrichment & footprinting; multi-species, MultiQC.
Quality Control, Mapping and Reads Count for RNA-Seq Analysis
A miniature example of a MultiQC plugin.
A Snakemake-based pipeline for processing and quality-controlling ancient and historical DNA data, including taxonomic assessment and comparative genomic analysis across time points, producing damage-rescaled, mapped reads ready for downstream analyses.
MultiQC plugin for the National Genomics Infrastructure in Stockholm, Sweden.
RNA-seq, smRNA-seq, scRNA-seq & ATAC-seq workflows for @cornell-TREX
Mini-game used instead of slides at my keynote at scverse 2016
MultiQC plugin dedicated to interact and analyze neuroimaging outputs.
This is an automated workflow pipeline for analyzing and processing Bulk-RNA seq data, implemented primarily in bash, python and R, and wrapped in a NextFlow workflow to characterize the gene landscape in the samples.
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