All Published Workflows

6 workflows that have been reviewed and published

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
affymetrix_cnv_pipeline
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Snakemake pipeline for calling CNAs from Affymetrix (now Thermofisher) Cytoscan and Oncoscan arrays
public

public

This pipeline has been adapted from https://github.com/gustaveroussy/EaCoN. It leverages the EaCoN R package to conduct p...
TxDb.Hsapiens.UCSC.hg19.knownGene Biobase GenomicRanges S4Vectors Snakemake SummarizedExperiment data.table qs EaCoN
Free
10
atac-seq
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ATAC-seq Data Analysis Workflow
public

public

#Snakemake workflow: ATAC-seq This is using the standard Snakemake workflow template. Replace this text with a comprehensive ...
BSgenome.Hsapiens.UCSC.hg19 BSgenome.Mmusculus.UCSC.mm10 TxDb.Hsapiens.UCSC.hg19.knownGene TxDb.Mmusculus.UCSC.mm10.knownGene macs2 PCAtools ROTS Rsamtools ATACseqQC BEDTools ChIPpeakAnno DESeq2 FeatureCounts homer MotifDb MultiQC Picard Rsubread SAMtools Snakemake STAR dplyr ggplot2 mgsub Trim_Galore ATAC-seq
Free
37
mpra-gwas-builder
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MPRA GWAS Builder: snakemake workflow
public

public

Robin Meyers (@robinmeyers) If you simply want to use this workflow, download and extract the latest release . If ...
BSgenome.Hsapiens.NCBI.GRCh38 BSgenome.Hsapiens.UCSC.hg19 SNPlocs.Hsapiens.dbSNP144.GRCh37 TxDb.Hsapiens.UCSC.hg19.knownGene TxDb.Hsapiens.UCSC.hg38.knownGene ucsc-liftover Biostrings Greedy algorithm for Set Cover problem haploR LDlinkR plyranges rtracklayer Snakemake VariantAnnotation cowplot doMC ggplot2 magrittr tidyverse
Free
17
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