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

FASTQ raw sequence reads Filtering Count matrix DeepTools FeatureCounts htseqcount SAMtools Snakemake STAR RNA-Seq

genrich BEDTools DeepTools pRESTO SAMtools Seurat Snakemake docopt Matrix tidyverse pysam

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

macs2 Bowtie 2 DeepTools fastp SAMtools Snakemake Trimmomatic

macs2 BEDTools Bowtie 2 Consensus DeepTools fastp homer MultiQC Pandas Pybedtools SAMBLASTER SAMtools Snakemake UROPA matplotlib numpy rpy2 scipy seaborn sklearn statsmodels umap

macs2 tabix BEDTools DeepTools SAMtools Snakemake

Sample annotation Trajectory visualization Alignment DeepTools SAMtools Snakemake RNA-Seq

nanofilt nanostat DeepTools FastQC Minimap2 MultiQC NanoPlot nanopolish Picard SAMtools Snakemake graphmap2 pycoQC

gatk tabix DeepTools FastQC MultiQC Quant Salmon SAMtools seqtk Snakemake SortMeRNA STAR vt Trim_Galore

MACS2 macs2 BWA DeepTools Sambamba SAMBLASTER SAMtools Snakemake