All Published Workflows

14 workflows that have been reviewed and published

pyflow-chipseq
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a snakemake pipeline to process ChIP-seq files from GEO or in-house
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public

a snakemake pipeline to process ChIP-seq files from GEO I have so many people asking me to process a public GEO ChIP-seq data...
Database metadata Peak calling Plot macs2 BEDTools Bowtie 2 DeepTools FastQC MultiQC Sambamba SAMBLASTER SAMtools Snakemake ChIP-seq
Free
17
chipseq
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ChIP-seq peak-calling, QC and differential analysis pipeline (Snakemake port of the nextflow pipeline at https://nf-co.re/chipseq).
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public

This is the template for a new Snakemake workflow. Replace this text with a comprehensive description covering the purpose an...
Data Peak calling Quality control report bedGraphToBigWig BEDTools BiocParallel BWA Cutadapt DESeq2 FastQC FeatureCounts GFFutils homer MaCS MultiQC Pandas pheatmap Picard SAMtools Snakemake UpSetR vsn ggplot2 lattice optparse RColorBrewer reshape2 scales tidyverse pysam PyYAML smart-open ChIP-seq
Free
117
cd4-csaw
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Reproducible reanalysis of a combined ChIP-Seq & RNA-Seq data set
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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
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atac-seq-pipeline
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ATAC-Seq and ChIP-Seq Analysis Pipeline for Chromatin Accessibility
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public

This pipeline is designed to take a set of input BAM files and perform ATAC-seq/chip-seq analysis on the data. The pipeline w...
macs2 BCRANK Biostrings Consensus DeepTools Snakemake ChIP-seq
Free
11
chipseq-snakemake
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Snakemake workflow: chipseq
public

public

This is the template for a new Snakemake workflow. Replace this text with a comprehensive description covering the purpose an...
bedGraphToBigWig BEDTools BiocParallel BWA Cutadapt DESeq2 FastQC FeatureCounts GFFutils homer MaCS MultiQC Pandas pheatmap Picard SAMtools Snakemake UpSetR vsn ggplot2 lattice optparse RColorBrewer reshape2 scales tidyverse pysam PyYAML smart-open ChIP-seq Sequence analysis
Free
117
smk_chipseq
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ChIPseq Data Processing Workflow with Snakemake
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public

This workflow performs some genernal data process for ChIPseq Please make sure that Snakemake and Git are correctly installed...
macs2 snakemake-wrapper-utils PCAtools Bowtie 2 DeepTools FastQC SAMtools Snakemake Trimmomatic dplyr ChIP-seq
Free
21
ngs-workflow-chipseq
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Basic ChIP-seq Analysis Workflow with Snakemake
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public

This repository contains a Snakemake workflow for performing a basic ChIP-seq analysis pipeline. This workflow was adapted fr...
snakemake-wrapper-utils Bowtie 2 DeepTools GenomicRanges rtracklayer Sambamba SAMtools seqkit Snakemake tidyverse ChIP-seq
Free
47
preparechips
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Snakemake workflow template for preparing single-end ChIP-Seq data
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public

This is a simple snakemake workflow template for preparing single-end ChIP-Seq data. The steps implemented are: D...
macs2 snakemake-wrapper-utils AdapterRemoval bedGraphToBigWig FastQC GLUE MultiQC SAMtools Snakemake magrittr tidyverse yaml ChIP-seq
Free
28
peaks_workflow
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Peaks Workflow for ChIP-seq, CUT&RUN, and ATAC-seq Data
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public

This workflow is designed to align, perform basic QC and call peaks for peak-based methods such as ChIP-seq, CUT&RUN and ATAC...
macs2 preseq ucsc-bedclip PCAtools Rsamtools BamTools bedGraphToBigWig Bedops BEDTools BiocParallel BWA ChIPpeakAnno csaw DeepTools DESeq2 DiffBind FastQC GenomeInfoDb MultiQC QualiMap rtracklayer SAMBLASTER SAMtools Snakemake dplyr magrittr readr stringr tibble viridis Trim_Galore ATAC-seq ChIP-seq
Free
52
chip-seq
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ChIP-seq
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public

A Snakemake workflow for ChIP-seq reads alignments with bwa , samtools and deeptools .
raw sequence reads Alignment Report BWA DeepTools FastQC MultiQC SAMtools Snakemake ChIP-seq
Free
17
atac_metacell_utilities
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Snakemake pipeline for scATAC metacell utilities such as primed and lineage specific scores, chromVAR, in-silico ChIP
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This repository contains a snakemake pipeline for utilities with ATAC and RNA metacells inferred using SEACells algor...
Sample ID Peak calling Gene expression matrix FiMO Pandas SCANPY Snakemake renv numpy scipy SEACells tqdm ChIP-seq
Free
22
bigr_epicure_pipeline
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Snakemake pipeline for Epicure analyses
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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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