All Published Workflows

6 workflows that have been reviewed and published

dropseqpipe
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A SingleCell RNASeq pre-processing snakemake workflow
public

public

This pipeline is based on snakemake and the dropseq tools provided by the McCarroll Lab . It allows to go from raw da...
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
Free
82
scmixture
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Mixture Model for Zero-Inflated scRNA-seq Data Analysis
public

public

A Bayesian mixture model approach to zero-inflation of counts for scRNA-seq data --- Table of Contents About ...
scran Snakemake ggplot2 gprofiler2 htmlwidgets plotly umap scRNAseq data processing
Free
16
single-cell-rna-seq
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Snakemake scRNAseq: A single cell RNA-seq workflow
public

public

A single cell RNA-seq workflow following Lun, McCarthy and Marioni 2016 and Soneson and Robinson 2018 , with added mo...
PCAtools CellAssign ComplexHeatmap edgeR limma RBGL Rgraphviz scater scran SingleCellExperiment Snakemake TensorFlow dplyr ggplot2 ggpubr ggsci gplots RColorBrewer tidyverse viridis scRNAseq data processing
Free
40
scrnaseq-snakemake
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Snakemake workflow: 10X single-cell + LARRY
public

public

A Snakemake workflow to process single-cell libraries generated with 10XGenomics platform (RNA, ATAC and RNA+ATAC) together w...
Sample ID Sequencing quality control Quality control report scDblFinder BiocParallel Biopython Consensus DropletUtils Pandas Seurat Signac SingleCellExperiment Snakemake ggplot2 tidyverse viridis scRNAseq data processing
Free
55
scrnaseq-single-sample-processing-starsolo
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scRNAseq Single Sample Processing STARSolo
public

public

From the R1 and R2 fastq files of a single samples, make a scRNAseq counts matrix, and perform basic QC with scanpy. Then, do...
FASTQ paired sequencing data Clustering Gene expression matrix Sample annotation ANN-SoLo Galaxy SCANPY WorkflowHub scRNAseq data processing
Free
polya_liftover
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polya_liftover sc/snRNAseq Snakemake Workflow using PolyA_DB and UCSC Liftover with Cellranger.
public

public

polya_liftover - sc/snRNAseq Snakemake Workflow A Snakemake workflow for using PolyA_DB and UCSC Liftover with Cellranger...
bcl2fastq-nextseq demultiplexer ucsc-liftover Snakemake cellranger helpers scRNAseq data processing
Free
16