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.
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.
AlphaFold-based Protein Analysis Pipeline
Quality Control, Mapping and Reads Count for RNA-Seq Analysis
A miniature example of a MultiQC plugin.
MultiQC plugin for the National Genomics Infrastructure in Stockholm, Sweden.
RNA-seq, smRNA-seq, scRNA-seq & ATAC-seq workflows for @cornell-TREX
MultiQC plugin dedicated to interact and analyze neuroimaging outputs.
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.
Estimate fastq-formatted read abundace in RNA-Seq analysis with Kallisto
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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