Aggregate results from bioinformatics analyses across many samples into a single report.

A SingleCell RNASeq pre-processing snakemake workflow

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.

A pipeline to investigate horizontal gene transfer from NGS data

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

A miniature example of a MultiQC plugin.

Quality Control, Mapping and Reads Count for RNA-Seq Analysis

One liner tool to check the quality of your single-cell atlases.

MultiQC plugin for the National Genomics Infrastructure in Stockholm, Sweden.

RNA-seq workflow for UALBANY CFG - Demux, QC, Vis, Align, preProcess, DGE Calls

RNA-seq, smRNA-seq, scRNA-seq & ATAC-seq workflows for @cornell-TREX

MultiQC plugin dedicated to interact and analyze neuroimaging outputs.

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.

Map and post-process your bams for SNP calling