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

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

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

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

Sequence Genetic variation analysis genetic variants gatk hla-la rust-bio-tools tabix Arriba BCFtools BWA Cutadapt FreeBayes kallisto Microphaser NetMHCIIpan NetMHCpan Pandas Picard Quant razers3 SAMtools Snakemake STAR Strelka Variant Effect Predictor (VEP) vembrane Jinja2 numpy Varlociraptor Genomics

bigWig ucsc-liftover BiocParallel Biopython Biostrings BSgenome Consensus GenomicAlignments GenomicFeatures GenomicRanges HiTC Pandas Picard rtracklayer SAMtools Snakemake STAR Trimmomatic corrplot eulerr factoextra GGally ggplot2 ggpubr ggrepel gridExtra here kableExtra Matrix optparse plotly pROC readxl tidyverse numpy plotly

BLAST htseqcount IgBLAST Singularity Hub Snakemake STAR

Cutadapt FastQC MultiQC Sambamba SAMtools Snakemake STAR

Biopython fastp Pandas scVelo Snakemake SRA STAR numpy

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