All Published Workflows

4 workflows that have been reviewed and published

snakeatac
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A snakemake workflow to process ATAC-seq data
public

public

Yet another snakemake workflow for ATAC-seq data processing. This pipeline was created from code developed by: Crazy Ho...
BSgenome.Hsapiens.UCSC.hg38 BSgenome.Mmusculus.UCSC.mm10 TxDb.Hsapiens.UCSC.hg38.knownGene TxDb.Mmusculus.UCSC.mm10.knownGene macs2 Rsamtools ATACseqQC bedGraphToBigWig BEDTools Bowtie 2 FastQC GenomicAlignments GenomicScores SAMtools Snakemake STAR ggplot2 Trim_Galore
Free
33
mpra-gwas-builder
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MPRA GWAS Builder: snakemake workflow
public

public

Robin Meyers (@robinmeyers) If you simply want to use this workflow, download and extract the latest release . If ...
BSgenome.Hsapiens.NCBI.GRCh38 BSgenome.Hsapiens.UCSC.hg19 SNPlocs.Hsapiens.dbSNP144.GRCh37 TxDb.Hsapiens.UCSC.hg19.knownGene TxDb.Hsapiens.UCSC.hg38.knownGene ucsc-liftover Biostrings Greedy algorithm for Set Cover problem haploR LDlinkR plyranges rtracklayer Snakemake VariantAnnotation cowplot doMC ggplot2 magrittr tidyverse
Free
17
memeth
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A Snakemake workflow to analyse and visualise Illumina Infinium Methylation arrays
public

public

A Snakemake workflow to analyse Illumina methylation arrays Overview Installation Usage
org.Hs.eg.db TxDb.Hsapiens.UCSC.hg19.knownGene TxDb.Hsapiens.UCSC.hg38.knownGene PCAtools ChIPpeakAnno ComplexHeatmap DMRcate ExperimentHub GenomicRanges limma minfi rtracklayer Snakemake ggplot2 ggrepel plyr reshape2
Free
42
bigr_epicure_pipeline
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Snakemake pipeline for Epicure analyses
public

public

Snakemake pipeline for Epicure analyses: Chip-Seq, Atac-Seq, Cut&Tag, Cut&Run, MeDIP-Seq, 8-OxoG-Seq CLI-Usage ...
BSgenome.Hsapiens.UCSC.hg38 TxDb.Hsapiens.UCSC.hg38.knownGene FASTQ Data Peak calling Quality control report PCAtools Rsamtools ATACseqQC BEDTools BiocParallel ChIPpeakAnno DeepTools homer MotifDb rtracklayer Sambamba Snakemake ChIP-seq
Free
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