All Published Workflows

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

raw sequence reads Quantification Quality control report BWA FastQC gffread GFFutils HTSeq htseqcount kallisto MultiQC QualiMap Quant RSEM Salmon SAMtools Snakemake STAR Trim_Galore Gene expression

dropest dropseq_tools Snakemake STAR Gene expression Sequence analysis

umi_tools Cutadapt fastp Kraken kraken2 MultiQC SAMtools Snakemake Gene expression

FeatureCounts Snakemake PyYAML Gene expression

org.Mm.eg.db CSV Data Enrichment analysis GO-term enrichment data biomaRt EnhancedVolcano OmnipathR PCAtools AnnotationHub BiocParallel CARNIVAL clusterProfiler ComplexHeatmap Consensus decoupleR DESeq2 enrichplot ensembldb FeatureCounts GFFutils GLUE GSEA GSEABase mitch MultiQC Pandas patcHwork pheatmap PIANO progeny Snakemake UpSetR viper broom cowplot dplyr ggplot2 ggraph ggupset knitr magrittr msigdbr network openxlsx plyr purrr RColorBrewer readr reshape2 scales snowfall svglite tibble tidygraph tidyr tidyverse visNetwork Gene expression

PCAtools limma oligo pheatmap Snakemake ggforce ggplot2 ggrepel hexbin RColorBrewer scales Gene expression

Expression analysis Quantification AdapterRemoval FastQC Quant Salmon SAMtools Snakemake Gene expression

snakemake-wrapper-utils BUSCO FastQC MultiQC Pandas seqtk-trinity Snakemake Trimmomatic Gene expression

BWA Cutadapt GFFutils MultiQC Pandas SAMtools Snakemake STAR Gene expression

Snakemake Gene expression

FASTQ-illumina JSON raw sequence reads Sequence read processing Quality control report preseq Arriba Bowtie 2 Cutadapt FastQC gtftogenepred kraken2 Krona MultiQC Picard QualiMap RSEM SAMtools Snakemake STAR Telescope Gene expression