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

JSON User metadata Expression analysis Quality control report bedGraphToBigWig BEDTools Cutadapt FastQC MultiQC Quant Salmon SAMtools Snakemake STAR Trim_Galore RNA-Seq

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

Genome index Annotation Map BEDTools BLAST fastp FastQC GFF3 Rebase gffread HISAT2 Minimap2 RepeatMasker RepeatModeler SAMtools Snakemake StringTie RNA-Seq

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

Sample annotation Splicing analysis Snakemake STAR Compound libraries and screening RNA-Seq

RNA sequence Sequence read processing Sequence report bwakit crass Bowtie 2 BWA cloudSPAdes metaspades MultiQC MUMmer4 plasmidspades QUAST rnaspades RVDB-prot seqtk Snakemake SPAdes Trimmomatic Plant biology RNA-Seq

Sample annotation Trajectory visualization Alignment DeepTools SAMtools Snakemake RNA-Seq

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

biomaRt Cutadapt DESeq2 MultiQC Pandas SAMtools Snakemake STAR tidyverse RNA-Seq

FastQC MultiQC Quant Salmon Snakemake Trimmomatic RNA-Seq

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