All Published Workflows

28 workflows that have been reviewed and published

varca
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Use an ensemble of variant callers to call variants from ATAC-seq data
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A pipeline for running an ensemble of variant callers to predict variants from ATAC-seq reads. The entire pipeline is made up...
VCF Data Variant calling genetic variants delly macs2 tabix BCFtools BEDTools BWA Pandas SAMtools Snakemake BBmisc data.table dplyr ggplot2 parallelMap plyr R.devices matplotlib numpy pysam sklearn ATAC-seq deep learning
Free
39
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
Free
117
iguide
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Bioinformatic pipeline for identifying dsDNA breaks by marker based incorporation, such as breaks induced by designer nucleases like Cas9.
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Bioinformatic pipeline for processing iGUIDE and GUIDE-seq samples. iGUIDE is a pipeline written in snakemake for proc...
Data Read pre-processing Report Biostrings BSgenome BWA Quant SAMtools Snakemake magrittr DNA
Free
65
singlecellproteogenomics
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Cell cycle analysis of single-cell proteomic and transcriptomic data for the FUCCI cell model
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This repository contains the code used to perform the single-cell proteogenomic analysis of the human cell cycle . This s...
Data Cell migration analysis Gene report Pandas SCANPY Snakemake matplotlib numpy scipy seaborn Proteogenomics
Free
10
salmon_deseq2_snakemake
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This repository has snakemake scripts for salmon-deseq2 pipeline for RNAseq data analysis
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RNAseq data analysis by Salmon-DESeq2 and Salmon-Wasabi-Sleuth pipelines are available here. RNAseq Data is availble from G...
FASTQ Data Quantification Quality control report PCAtools tximport apeglm Cutadapt DESeq2 FastQC MultiQC pheatmap Quant regionReport Salmon sleuth Snakemake vsn ggplot2 readr stringr RNA-Seq
Free
9
lcwgs-imputation-workflow
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Imputation workflow for low coverage whole genome sequencing data
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This workflow is for imputation using low coverage whole genome sequencing data with QUILT . Also, it can perform benchma...
Data Imputation Genome report tabix BCFtools SAMtools Snakemake Whole genome sequencing
Free
55
bwa_mem_mapping
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Fastq to bam mapping pipeline with marked duplicates, indexing, and insert size metric collection
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Fastq to bam mapping pipeline with marked duplicates, indexing, and insert size metric collection This is a Snakemake-based p...
Data Analysis Report BWA SAMBLASTER SAMtools Snakemake Data identity and mapping
Free
7
cite-seq-alevin-fry-seurat
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Snakemake workflow for CITE-seq analaysis with alevin-fry and seurat
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This workflow is untested and work in progress. It is based on this tutorial .
Data Analysis Report Quant Salmon Seurat SingleCellExperiment Snakemake devtools ggplot2 Matrix rjson pybiomart Data quality management
Free
27
fastcn-smk
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A snakemake for fastCN reference setup
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The Snakefile is under workflow . Most installing is done by Snakemake but there is one small Makefile. Please re...
Data Alignment Count matrix rustybam BEDTools mrsFAST Pandas SAMtools seqtk Snakemake fastCN numba pysam Data quality management
Free
33
googlemags
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Workflow for MAG construction
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Workflow for MAG construction snakemake -p --verbose --keep-remote -j [number of available cores] --kubernetes -s Snakefile...
Data Analysis Report MEGAHIT BWA Cutadapt SAMtools Snakemake Data quality management
Free
5
snakemake_fastqc_mothur
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Second workflow that takes the output of the guppy workflow to run fastqc and create a multiQC report. Then run Mothur for analysis.
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This workflow takes the output from the GUPPY workflow and runs fastqc, multiqc, and mothur. Hans Vasquez-Gross Lucas...
Data Sequencing quality control Quality control report FastQC mothur MultiQC Snakemake Function analysis
Free
9
multicondition-deseq2-enrichment
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Workflow dervied form https://github.com/snakemake-workflows/rna-seq-star-deseq2 for multi condition Deseq2 and enrichment analyis
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Snakemake workflow for running differential expression and enrichment analyses for experimental setups with multiple groups o...
org.Mm.eg.db CSV Data Enrichment analysis GO-term enrichment data biomaRt EnhancedVolcano OmnipathR PCAtools AnnotationHub BiocParallel CARNIVAL clusterProfiler ComplexHeatmap Consensus decoupleR DESeq2 enrichplot ensembldb FeatureCounts GFFutils GLUE GSEA GSEABase mitch MultiQC Pandas patcHwork pheatmap PIANO progeny Snakemake UpSetR viper broom cowplot dplyr ggplot2 ggraph ggupset knitr magrittr msigdbr network openxlsx plyr purrr RColorBrewer readr reshape2 scales snowfall svglite tibble tidygraph tidyr tidyverse visNetwork Gene expression
Free
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