All Published Workflows

Database metadata Peak calling Plot macs2 BEDTools Bowtie 2 DeepTools FastQC MultiQC Sambamba SAMBLASTER SAMtools Snakemake ChIP-seq

Expression data Peak calling Plot macs2 ataqv BEDTools Bowtie 2 DeepTools FastQC MultiQC SAMBLASTER SAMtools Snakemake ATAC-seq

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

BSgenome.Hsapiens.UCSC.hg19 BSgenome.Hsapiens.UCSC.hg38 Gene ID Peak calling Quality control report macs2 ucsc-liftover BEDTools BiocParallel Bowtie 2 csaw Cufflinks GenomicAlignments GenomicRanges GLUE graphite GSEABase HISAT2 kallisto Quant rtracklayer Salmon SAMtools Snakemake SRAdb STAR SummarizedExperiment assertthat dplyr forcats future getopt ggforce ggplot2 here ks magrittr optparse reshape2 rex rlang scales stringr rpy2 rctutils ChIP-seq

Sample ID Peak calling Gene expression matrix FiMO Pandas SCANPY Snakemake renv numpy scipy SEACells tqdm ChIP-seq

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

Sample ID Peak calling Plot macs2 bedGraphToBigWig SAMtools Snakemake Genomics

FASTQ-illumina FASTQ-sanger raw sequence reads Peak calling Report Bowtie 2 Cutadapt Galaxy illumina MACS MultiQC SAMtools WorkflowHub Biological databases

FASTQ-sanger CleanEx dataset code Peak calling Quality control report BEDTools Bowtie 2 Cutadapt Galaxy MACS MultiQC SAMtools WorkflowHub Genomics

FASTQ raw sequence reads Peak calling Quality control report macs2 BEDTools Bowtie 2 Cutadapt DeepTools FastQC MultiQC SAMtools ChIP-seq