All Published Workflows

9 workflows that have been reviewed and published

cd4-csaw
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Reproducible reanalysis of a combined ChIP-Seq & RNA-Seq data set
public

public

This is the code for a re-analysis of a [GEO dataset][1] that I originally analyzed for [this paper][2] using statistical met...
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
Free
114
signac-paper
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Code to reproduce analyses shown in the Signac paper
public

public

Code to reproduce analyses shown in Stuart et al. 2021, Nature Methods To run the workflow, first create a new conda envi...
BSgenome.Hsapiens.UCSC.hg38 EnsDb.Hsapiens.v75 EnsDb.Mmusculus.v79 macs2 tabix DropletUtils GenomeInfoDb GenomicRanges patcHwork Seurat Signac Snakemake cluster dplyr future ggplot2 Matrix mclust paletteer RANN tidyr SeuratDisk
Free
61
snakeatac
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A snakemake workflow to process ATAC-seq data
public

public

Yet another snakemake workflow for ATAC-seq data processing. This pipeline was created from code developed by: Crazy Ho...
BSgenome.Hsapiens.UCSC.hg38 BSgenome.Mmusculus.UCSC.mm10 TxDb.Hsapiens.UCSC.hg38.knownGene TxDb.Mmusculus.UCSC.mm10.knownGene macs2 Rsamtools ATACseqQC bedGraphToBigWig BEDTools Bowtie 2 FastQC GenomicAlignments GenomicScores SAMtools Snakemake STAR ggplot2 Trim_Galore
Free
33
nanobody
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Nanobody-tethered transposition followed by sequencing
public

public

This repository contains code needed to reproduce the analyses shown in Stuart et al. (2022), Nature Biotechnology Mo...
BSgenome.Hsapiens.UCSC.hg38 EnsDb.Hsapiens.v86 tabix Rsamtools tximport bedGraphToBigWig BEDTools Biopython Bwa-mem2 Cutadapt DeepTools GenomeInfoDb GenomicRanges patcHwork Quant Salmon SAMtools Seurat Signac Snakemake SummarizedExperiment dplyr future ggplot2 ggtern Matrix RANN RColorBrewer RcppRoll pysam SeuratWrappers
Free
87
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
cfmedipseq_pipeline
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cfMeDIP-seq Circulating Methylome Data Post-processing Pipeline
public

public

Post-processing pipeline for next-generation circulating methylome data generated by cfMeDIP-seq The only up-front dependency...
BSgenome.Hsapiens.UCSC.hg38 BiocParallel BSgenome BWA FastQC GenomicRanges IRanges MEDIPS qsea SAMtools Snakemake docopt flexmix MASS Rcpp tidyverse countreg Trim_Galore Sequence analysis
Free
37
plbr_medremixbedpe
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Run MedRemix with bedpe input as part of PLBR database workflow
public

public

Run MedRemix methylation profiler with bedpe input as part of PLBR database workflow. Pipeline is an extension of the ...
BSgenome.Hsapiens.UCSC.hg38 BWA FastQC GTools MEDIPS Picard SAMtools Snakemake arrow docopt doParallel plyr readr tidyverse pysam Trim_Galore
Free
33
plbr_medestrandbedpe
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Run MeDEStrand with bedpe input as part of PLBR database workflow
public

public

Run MeDEStrand methylation profiler with bedpe input as part of PLBR database workflow. Pipeline is an extension of OI...
BSgenome.Hsapiens.UCSC.hg38 umi_tools BWA FastQC GenomicRanges GTools MEDIPS Picard SAMtools Snakemake docopt tidyverse pysam
Free
38
bigr_epicure_pipeline
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Snakemake pipeline for Epicure analyses
public

public

Snakemake pipeline for Epicure analyses: Chip-Seq, Atac-Seq, Cut&Tag, Cut&Run, MeDIP-Seq, 8-OxoG-Seq CLI-Usage ...
BSgenome.Hsapiens.UCSC.hg38 TxDb.Hsapiens.UCSC.hg38.knownGene FASTQ Data Peak calling Quality control report PCAtools Rsamtools ATACseqQC BEDTools BiocParallel ChIPpeakAnno DeepTools homer MotifDb rtracklayer Sambamba Snakemake ChIP-seq
Free
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