All Published Workflows

183 workflows that have been reviewed and published

rna-seq-star-deseq2
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RNA-seq workflow using STAR and DESeq2
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This workflow performs a differential gene expression analysis with STAR and Deseq2. The usage of this workflow is described ...
raw sequence reads Gene expression profiling ID list snakemake-wrapper-utils biomaRt PCAtools BiocParallel BWA Cutadapt DESeq2 GFFutils MultiQC Pandas SAMtools Snakemake STAR cli stringr tidyverse RNA-Seq
Free
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single-cell-rna-seq
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A single cell RNA-seq workflow, including highly variable gene analysis, cell type assignment and differential expression analysis.
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A single cell RNA-seq workflow following Lun, McCarthy and Marioni 2016 and Soneson and Robinson 2018 , with added mo...
PCAtools CellAssign ComplexHeatmap edgeR limma RBGL Rgraphviz scater scran SingleCellExperiment TensorFlow dplyr ggplot2 ggpubr ggsci gplots RColorBrewer tidyverse viridis
Free
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rna-seq-kallisto-sleuth
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A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.
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A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth . The usage of thi...
JSON Expression data Expression analysis Expression data bioawk snakemake-wrapper-utils biomaRt IHW Biopython BWA CPAT Cutadapt fgsea graphite GSEA IsoformSwitchAnalyzeR kallisto limma Pandas pheatmap Picard Quant SAMtools sleuth Snakemake SPIA dplyr fs ggplot2 ggpubr gridExtra tidyr tidyverse altair altair-saver goatools matplotlib numpy pysam scipy RNA-Seq
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score-assemblies
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Score and compare multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s)
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A snakemake-wrapper for evaluating de novo bacterial genome assemblies, e.g. from Oxford Nanopore (ONT) or Illumina seque...
bacterial Genome assembly Genome report nucdiff prodigal Bakta BUSCO Diamond Minimap2 QUAST SAMtools seqkit Snakemake ggplot2 tidyverse Comparative genomics nanopore
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chipseq
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ChIP-seq peak-calling, QC and differential analysis pipeline (Snakemake port of the nextflow pipeline at https://nf-co.re/chipseq).
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This is the template for a new Snakemake workflow. Replace this text with a comprehensive description covering the purpose an...
Data Peak calling Quality control report bedGraphToBigWig BEDTools BiocParallel BWA Cutadapt DESeq2 FastQC FeatureCounts GFFutils homer MaCS MultiQC Pandas pheatmap Picard SAMtools Snakemake UpSetR vsn ggplot2 lattice optparse RColorBrewer reshape2 scales tidyverse pysam PyYAML smart-open ChIP-seq
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haplotyped-methylome
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Reproducibility workflow for Gigante et al., 2018: Using long-read sequencing to detect imprinted DNA methylation
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Reproducibility instructions for Gigante et al., 2019. Note: this repository is still being tested! If you find a bug, plea...
snpsplit Biopython bsseq BWA DSS GenomicRanges HISAT2 nanopolish SAMtools Snakemake Bismark broom data.table dplyr magrittr readr tidyverse numpy pysam Trim_Galore
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rna-seq-pop
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Snakemake workflow for Illumina RNA-sequencing experiments - extract population genomic signals from RNA-Seq data
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Documentation : https://sanjaynagi.github.io/rna-seq-pop/ Walkthrough : https://www.youtube.com/watch?v=5QQe7DLHO4...
FASTQ-illumina JSON Sample annotation Variant calling genetic variants snakemake-wrapper-utils EnhancedVolcano BCFtools DESeq2 fastp FreeBayes GLUE HISAT2 kallisto mosdepth MultiQC Pandas pheatmap Quant SAMBLASTER SAMtools sleuth Snakemake snpEff Vcflib data.table dplyr ggplot2 ggrepel jsonlite openxlsx RColorBrewer tidyverse ipykernel matplotlib matplotlib-venn numpy papermill pop-tools scipy zarr Population genomics
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pyflow-scatacseq
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snakemake workflow for post-processing scATACseq data
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snakemake workflow for post-processing scATACseq data cite if you use it:) for single cell ATACseq experiment, one gets a mer...
genrich BEDTools DeepTools pRESTO SAMtools Seurat Snakemake docopt Matrix tidyverse pysam
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mikropml-snakemake-workflow
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Snakemake template for building reusable and scalable machine learning pipelines with mikropml
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Snakemake is a workflow manager that enables massively parallel and reproducible analyses. Snakemake is a suitable tool to...
patcHwork Snakemake dplyr ggplot2 knitr mikropml readr schtools tidyverse
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cuttag-pipeline
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Pipeline for Cut&Tag analysis
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Snakemake pipeline for Cut&Tag analysis # cd into a project directory # type the following to get a copy of the pipeline git ...
preseq ucsc-bigwigmerge ucsc-bigwigtobedgraph PCAtools bedGraphToBigWig BEDTools Bowtie 2 Consensus DeepTools DESeq2 fastp FastQC MultiQC Pandas pheatmap plyranges Sambamba SAMtools Snakemake vsn dendextend ggplot2 ggrepel gplots PoiClaClu RColorBrewer tidyr tidyverse plotly
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tapseq_manuscript
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Analysis code for the TAP-seq manuscript.
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This repository contains code to reproduce the results presented in the article. It builds upon a snakemake workflow that...
bigWig ucsc-liftover BiocParallel Biopython Biostrings BSgenome Consensus GenomicAlignments GenomicFeatures GenomicRanges HiTC Pandas Picard rtracklayer SAMtools Snakemake STAR Trimmomatic corrplot eulerr factoextra GGally ggplot2 ggpubr ggrepel gridExtra here kableExtra Matrix optparse plotly pROC readxl tidyverse numpy plotly
Free
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bo-demography
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Demographic analysis of Brassica oleracea
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Demographic analysis of Brassica oleracea Follows GATK4 best practices (https://software.broadinstitute.org/gatk/best-practic...
gatk tabix BCFtools BEDTools BWA CLICK FastQC MultiQC Pandas QualiMap SAMtools Snakemake VCFtools cowplot ggplot2 tidyverse
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