All Published Workflows

12 workflows that have been reviewed and published

bulk-rnaseq
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Workflow to process bulk RNASeq samples using Salmon and DESeq2
public

public

Simple workflow to quantify gene-level RNA abundance and detect differentially expressed genes (DEGs) from bulk RNAseq sample...
org.Hs.eg.db biopet-validatefastq IHW PCAtools BiocParallel DESeq2 FastQC MultiQC Pandas Quant Salmon Singularity Hub Snakemake tximeta dplyr ggplot2 readr stringr
Free
13
eacon_cnv_pipeline
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Easy Copy Number Analysis (EaCoN) Pipeline
public

public

This pipeline has been adapted from https://github.com/gustaveroussy/EaCoN. It leverages the EaCoN R package to conduct p...
BSgenome.Hsapiens.UCSC.hg38 org.Hs.eg.db TxDb.Hsapiens.UCSC.hg19.knownGene Biobase BiocParallel GenomicRanges RaggedExperiment Snakemake data.table qs EaCoN
Free
13
cluster_rnaseq
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cluster_rnaseq: RNA-seq pipeline.
public

public

Pipeline status cluster_rnaseq is a Snakemake pipeline that performs a comprehensive RNA-seq analysis, coverin...
org.Hs.eg.db snakemake-wrapper-utils AnnotationDbi BBMap BiocParallel Bowtie 2 ComplexHeatmap DESeq2 FastQC FeatureCounts HISAT2 htseqcount limma MultiQC Pandas patcHwork pheatmap Quant Salmon SAMtools seqtk Snakemake STAR tximeta dplyr ggplot2 ggpubr ggrepel openxlsx plyr RColorBrewer readr scales stringr tibble tidyr numpy
Free
58
merfishtools-evaluation
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The evaluation of MERFISHtools and the underyling model as published in the corresponding article.
public

public

This Snakemake workflow generates the entire analysis of the forthcoming manuscript "A Bayesian model for single cell transcr...
GO.db org.Hs.eg.db merfishtools biomaRt BiocSklearn GOstats Pandas Snakemake mutoss bitarray common matplotlib networkx numpy scipy seaborn sklearn svgutils
Free
95
rnaseq-salmon-deseq2
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RNA-Seq Analysis Workflow with Snakemake
public

public

流程管理 : snakemake 软件 版本 功能 mulitqc 数据质控 salmon RNA-Seq 定量 DEseq2 差异分析 . ├── README.md #流程描述文件 ├── config.yaml #流程参数文件 ├── ...
org.Hs.eg.db tximport apeglm BiocParallel clusterProfiler DESeq2 FastQC MultiQC pheatmap Quant rtracklayer Salmon Snakemake dplyr ggpubr readr stringr tidyverse RNA-Seq
Free
24
genesetenrichment
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Snakemake pipeline for Gene Set Enrichment: pathway and GO enrichment analysis
public

public

Author: Sherine Awad Change the config.yaml file appropriately according to your data. Update parameters of Genrich in the co...
org.Hs.eg.db org.Mm.eg.db biomaRt AnnotationDbi edgeR gage pathview Snakemake data.table dplyr gplots magrittr
Free
4
kas-seq-workflow
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KAS-Seq Analysis Workflow
public

public

Workflow to perform KAS-seq analysis This is the template for a new Snakemake workflow. Replace this text with a comprehensiv...
org.Hs.eg.db snakemake-wrapper-utils AnnotationDbi BWA ChIPseeker Cutadapt DeepTools FastQC GenomicFeatures MultiQC PACMAN Picard SAMtools Snakemake argparser BiocManager cowplot dplyr ggplot2 readr
Free
45
bulk-rnaseq
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Bulk RNA-seq Analysis Pipeline for Differentially Expressed Genes (DEGs)
public

public

Simple workflow to quantify gene-level RNA abundance and detect differentially expressed genes (DEGs) from bulk RNAseq sample...
org.Hs.eg.db biopet-validatefastq IHW PCAtools BiocParallel DESeq2 FastQC MultiQC Pandas Quant Salmon Singularity Hub Snakemake tximeta dplyr ggplot2 readr stringr RNA-Seq Sequence analysis
Free
13
memeth
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A Snakemake workflow to analyse and visualise Illumina Infinium Methylation arrays
public

public

A Snakemake workflow to analyse Illumina methylation arrays Overview Installation Usage
org.Hs.eg.db TxDb.Hsapiens.UCSC.hg19.knownGene TxDb.Hsapiens.UCSC.hg38.knownGene PCAtools ChIPpeakAnno ComplexHeatmap DMRcate ExperimentHub GenomicRanges limma minfi rtracklayer Snakemake ggplot2 ggrepel plyr reshape2
Free
42
snakesplice
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A Snakemake based modular Workflow that facilitates RNA-Seq analyses with a special focus on splicing
public

public

A Snakemake based modular Workflow that facilitates RNA-Seq analyses with a special focus on the exploration of differential ...
org.Hs.eg.db TxDb.Hsapiens.UCSC.hg19.knownGene snakemake-wrapper-utils PCAtools tximport AnnotationDbi apeglm Arriba BEDTools BiocParallel clusterProfiler Cufflinks cummeRbund DESeq2 enrichplot FastQC FeatureCounts FRASER genefilter GFFutils GSEA HTSeq htseqcount kallisto kraken2 MultiQC OUTRIDER Pandas pheatmap Quant regtools ReportingTools rhdf5 RSEM Salmon SAMtools Snakemake STAR SummarizedExperiment Trimmomatic tximeta data.table dplyr ggplot2 ggpubr knitr lattice magrittr plotly PoiClaClu RColorBrewer plotly
Free
160
cnmf_pipeline
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A pipeline to connect GWAS Variant-to-Gene-to-Program (V2G2P) Approach
public

public

A pipeline to connect GWAS variants to genes to disease-associate gene programs. This pipeline uses snakemake and cNMF from ...
org.Hs.eg.db Variant filtering Spectra universalmotif BEDTools BiocSklearn Consensus DeepTools FiMO FOCUS ggseqlogo GSEA limma Magma Pandas SCANPY Seurat Snakemake cowplot data.table dplyr ggplot2 ggpubr ggrepel gplots Matrix optparse readxl reshape2 reticulate scales stringi stringr svglite tidyr xlsx yaml anndata cnmf matplotlib numpy PyYAML scipy sklearn GWAS study
Free
87
rnaseq-workflow
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Differential Gene Expression using RNA-Seq
public

public

RNAseq is becoming the one of the most prominent methods for measuring celluar responses. Not only does RNAseq have the abili...
GO.db org.Hs.eg.db org.Mm.eg.db Differential gene expression profiling biomaRt PCAtools clusterProfiler DESeq2 DOSE FastQC FeatureCounts gage genefilter MultiQC pathview pheatmap ReactomePA SortMeRNA STAR topGO dplyr ggplot2 ggsci knitr RColorBrewer Trim_Galore RNA-Seq
Free
44