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

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

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

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

scp Bowtie 2 BWA CheckM CRIMSON dRep FastQC Mash metaprokka MetaWRAP MultiQC SAMtools seqtk Snakemake SPAdes SRA ggplot2 gridExtra RColorBrewer tidyr gtdbtk

Pandas pLink Snakemake dplyr ggplot2 maps tidyr numpy

JSON dada2 Biopython Biostrings BLAST Bowtie 2 Cutadapt FastQC MultiQC phyloseq seqtk Snakemake subSeq Trimmomatic dplyr ggplot2 plyr stringr tibble tidyr worrms xml2 yaml

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

dada2 biomformat Biopython Biostrings Consensus Cutadapt DECIPHER edgeR FastQC Krona metagenomeSeq MultiQC Pandas PANDAseq phyloseq PICRUSt2 QIIME2.0 Snakemake SRA VSEARCH data.table dplyr ggplot2 magrittr plyr RColorBrewer reshape2 stringr tibble tidyr vegan

assembly-stats cooler BEDTools Biopython BLAST BUSCO cd-hit Diamond genomepy MaxBin Minimap2 NG-Circos OrthoFinder Pandas patcHwork QUAST seqkit Snakemake topGO dplyr ggplot2 gridExtra readr stringr tibble tidyr tidyverse viridis cooler matplotlib matplotlib-venn numpy reportlab seaborn

BSgenome.Hsapiens.UCSC.hg38 EnsDb.Hsapiens.v75 EnsDb.Mmusculus.v79 macs2 tabix DropletUtils GenomeInfoDb GenomicRanges patcHwork Seurat Signac Snakemake cluster dplyr future ggplot2 Matrix mclust paletteer RANN tidyr SeuratDisk