All Published Workflows

3 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
atac-seq
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ATAC-seq Data Analysis Workflow
public

public

#Snakemake workflow: ATAC-seq This is using the standard Snakemake workflow template. Replace this text with a comprehensive ...
BSgenome.Hsapiens.UCSC.hg19 BSgenome.Mmusculus.UCSC.mm10 TxDb.Hsapiens.UCSC.hg19.knownGene TxDb.Mmusculus.UCSC.mm10.knownGene macs2 PCAtools ROTS Rsamtools ATACseqQC BEDTools ChIPpeakAnno DESeq2 FeatureCounts homer MotifDb MultiQC Picard Rsubread SAMtools Snakemake STAR dplyr ggplot2 mgsub Trim_Galore ATAC-seq
Free
37
gr-mediated_gene_repression
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Code for the manuscript "Machine learning reveals STAT motifs as predictors for GR-mediated gene repression"
public

public

TODO: Add citation once paper is accepted Software dependencies
BSgenome.Mmusculus.UCSC.mm10 BSgenome.Mmusculus.UCSC.mm9 org.Mm.eg.db TxDb.Mmusculus.UCSC.mm10.knownGene macs2 biomaRt universalmotif BEDTools Bowtie 2 CAGEr ChIPpeakAnno ChIPseeker ComplexHeatmap Consensus Cutadapt DeepTools DESeq2 FastQC FiMO genomation GenomicRanges MEME memes MultiQC Picard plyranges rtracklayer SAMtools Snakemake topGO circlize data.table dplyr ggplot2 ggpubr glmnet here optparse plsgenomics plyr png RColorBrewer stringr
Free
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