All Published Workflows

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

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

Sample ID Analysis Report macs2 bedGraphToBigWig BEDTools Bowtie 2 BWA DeepTools FastQC homer Pandas Sambamba SAMtools Snakemake Trimmomatic ATAC-seq

macs2 Bowtie 2 FastQC Picard SAMtools Snakemake Trimmomatic ATAC-seq Sequence analysis

macs2 BEDTools Bowtie 2 Cutadapt DeepTools FastQC Picard SAMtools Snakemake ATAC-seq

macs2 Bowtie 2 Cutadapt FastQC Picard SAMtools Snakemake ATAC-seq

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

macs2 BEDTools Bowtie 2 DeepTools FastQC Picard SAMtools Snakemake ATAC-seq

macs2 snakemake-wrapper-utils PCAtools Bowtie 2 DeepTools FastQC SAMtools Snakemake Trimmomatic ATAC-seq

ngmerge snakemake-wrapper-utils Bowtie 2 DeepTools DESeq2 FeatureCounts GenomicRanges rtracklayer Sambamba SAMtools seqkit Snakemake tidyverse ATAC-seq

macs2 preseq ucsc-bedclip PCAtools Rsamtools BamTools bedGraphToBigWig Bedops BEDTools BiocParallel BWA ChIPpeakAnno csaw DeepTools DESeq2 DiffBind FastQC GenomeInfoDb MultiQC QualiMap rtracklayer SAMBLASTER SAMtools Snakemake dplyr magrittr readr stringr tibble viridis Trim_Galore ATAC-seq ChIP-seq

bigWig chromap macs2 preseq umi_tools ataqv BamTools bedGraphToBigWig BEDTools Bowtie 2 BWA DeepTools DESeq2 FastQC FeatureCounts gffread GFFutils homer khmer MultiQC Nextflow Picard SAMtools STAR Trim_Galore ATAC-seq