All Published Workflows

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

JSON bracken BBMap Bowtie 2 fastp FeatureCounts humann Kaiju Kraken kraken2 KrakenUniq Krona MetaPhlAn MultiQC Pandas SAMtools Singularity Hub Snakemake matplotlib numpy seaborn

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

Barrnap prodigal MEGAHIT Biopython BLAST Bowtie 2 Centrifuge CheckM contigtax Cutadapt edgeR eggNOG-mapper v2 FastANI FastQC FeatureCounts Infernal cmscan (EBI) kraken2 Krona MaxBin MetaBAT 2 metagenomeSeq MetaPhlAn metaspades MultiQC Pandas Picard SAMtools seqtk Snakemake SortMeRNA SqueezeMeta Trimmomatic Trnascan-SE CONCOCT common gtdbtk networkx numpy RGI

Sequence Sequence annotation ORF ID gatk ucsc-bigwigtowig BEDTools Cutadapt FastQC FeatureCounts GFFutils MultiQC Picard SAMtools Snakemake wigToBigWig bacterial assembly and annotation

prodigal MEGAHIT Bowtie 2 fastp FeatureCounts SAMtools Snakemake

tabix umi_tools BEDTools Bowtie 2 FastQC FeatureCounts MAnorm MultiQC SAMtools Snakemake STAR

gatk tximport Arriba Cutadapt FastQC FeatureCounts GenomicFeatures GFFutils MultiQC Quant Salmon SAMtools Snakemake STAR

tabix umi_tools BEDTools Bowtie 2 FastQC FeatureCounts MAnorm MultiQC SAMtools Snakemake STAR

Sequence analysis biomaRt PCAtools BBMap Cutadapt DESeq2 FeatureCounts gffread Quant Salmon SAMtools Snakemake STAR devtools docopt ggplot2 tidyverse RNA-Seq

DESeq2 BLAST DESeq2 fastp FeatureCounts HISAT2 pheatmap SAMtools Snakemake StringTie apcluster calibrate cluster colorRamps dendextend dplyr dynamicTreeCut e1071 ggplot2 gplots optparse RColorBrewer reshape2 tidyr vegan numpy

FeatureCounts HISAT2 Pandas SAMtools Snakemake StringTie Trimmomatic RNA-Seq