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

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

FASTQ-illumina JSON Sample annotation Variant calling genetic variants snakemake-wrapper-utils EnhancedVolcano BCFtools DESeq2 fastp FreeBayes GLUE HISAT2 kallisto mosdepth MultiQC Pandas pheatmap Quant SAMBLASTER SAMtools sleuth Snakemake snpEff Vcflib data.table dplyr ggplot2 ggrepel jsonlite openxlsx RColorBrewer tidyverse ipykernel matplotlib matplotlib-venn numpy papermill pop-tools scipy zarr Population genomics

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

ANCOMBC Maaslin2 ALDEx2 Biobase biomformat DESeq2 edgeR metagenomeSeq Pandas phyloseq dplyr joblib matplotlib numpy seaborn sklearn UpSetPlot

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

DESeq2 SortMeRNA tximport AnnotationDbi BEDTools Bowtie 2 DESeq2 kallisto MashMap MultiQC Rsubread Salmon Snakemake SRA data.table

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

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

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

JSON ComplexHeatmap DESeq2 EDASeq edgeR Glimma HTSeq limma NOISeq Pandas rtracklayer Snakemake data.table dplyr ggplot2 ggpubr ggthemes gridExtra janitor magick png readr reshape2 tidyr requests