All Published Workflows

raw sequence reads Gene expression profiling ID list snakemake-wrapper-utils biomaRt PCAtools BiocParallel BWA Cutadapt DESeq2 GFFutils MultiQC Pandas SAMtools Snakemake STAR cli stringr tidyverse RNA-Seq

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

bacterial Labeled quantification Scatter plot plotting Plot bracken kraken2 Pandas Snakemake stringr numpy metagenomics

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

Snakemake data.table dplyr ggplot2 gridExtra plyr seqinr stringr

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

GenomeInfoDbData qusage slingshot BiocParallel Bowtie 2 FastQC GFFutils GSEA MultiQC patcHwork pheatmap SCANPY Seurat SingleCellExperiment Snakemake STAR cluster clustree data.table devtools dplyr future ggplot2 htmltools Matrix openxlsx RColorBrewer reticulate rgl rmarkdown scales stringr viridis SeuratDisk SeuratWrappers

BiocParallel DESeq2 kallisto Snakemake corrr cowplot ggplot2 ggsignif readr Rtsne stringr tidyverse

Query script Multiple sequence alignment Phylogenetic tree raxml-ng APE Bio3D Snakemake trimAl dplyr stringr ete3 Phylogeny

tabix Biopython Pandas Snakemake boot caret data.table dplyr ggplot2 gridExtra optparse pROC PRROC ranger readr readxl stringr tidyverse VennDiagram biographs biopandas networkx numpy pdbparser

FASTQ Data Quantification Quality control report PCAtools tximport apeglm Cutadapt DESeq2 FastQC MultiQC pheatmap Quant regionReport Salmon sleuth Snakemake vsn ggplot2 readr stringr RNA-Seq