All Published Workflows

raw sequence reads Read pre-processing Report umi_tools BBMap Biopython Cutadapt FastQC MultiQC Seurat Snakemake STAR devtools dplyr ggplot2 gridExtra Matrix plotly plyr RColorBrewer stringr tidyr viridis yaml pysam scRNAseq data processing

FASTQ Sample ID Alignment Count matrix Minimap2 Quant Salmon SAMtools Snakemake stageR dplyr ggplot2 tidyr Gene expression

PCAtools CellAssign ComplexHeatmap edgeR limma RBGL Rgraphviz scater scran SingleCellExperiment TensorFlow dplyr ggplot2 ggpubr ggsci gplots RColorBrewer tidyverse viridis

JSON Expression data Expression analysis Expression data bioawk snakemake-wrapper-utils biomaRt IHW Biopython BWA CPAT Cutadapt fgsea graphite GSEA IsoformSwitchAnalyzeR kallisto limma Pandas pheatmap Picard Quant SAMtools sleuth Snakemake SPIA dplyr fs ggplot2 ggpubr gridExtra tidyr tidyverse altair altair-saver goatools matplotlib numpy pysam scipy RNA-Seq

Database ID Taxonomic classification Plot bracken kraken-biom cmapR ALDEx2 Kraken kraken2 Krona Pandas Snakemake ggplot2 ggpubr RColorBrewer reshape2 vegan metagenomics

raw sequence reads Primer removal Quality control report dada2 BLAST cd-hit Cutadapt FastQC MultiQC Pandas PANDAseq seqtk ShortRead Snakemake Swarm VSEARCH AmpliconDuo data.table ggplot2 xtable dinopy numpy PyYAML tables Function analysis

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

bacterial Genome assembly Genome report nucdiff prodigal Bakta BUSCO Diamond Minimap2 QUAST SAMtools seqkit Snakemake ggplot2 tidyverse Comparative genomics nanopore

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

mosaicatcher tabix BCFtools BEDTools ComplexHeatmap Pandas pheatmap SAMtools Snakemake TensorFlow WhatsHap assertthat BiocManager cowplot data.table devtools dplyr ggnewscale ggplot2 ggpubr matrixStats optparse RColorBrewer reshape reshape2 scales stringr tibble tidyr intervaltree matplotlib numpy parmap plotly pysam PyYAML scipy seaborn tqdm xopen

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

bacterial Phylogenetic analysis Phylogenetic tree fasttree BamTools BEDTools BWA Consensus ggtree SAMtools Snakemake ggplot2 phangorn metagenomics