All Published Workflows
88 workflows that have been reviewed and published
![pyflow-chipseq](https://media.bioworkflows.com/bioworkflows/public_preview/f5d0818530af19dd55996539923676f2b46766184a02fac2f955df55637f8f62.jpg)
a snakemake pipeline to process ChIP-seq files from GEO or in-house
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...
![pyflow-atacseq](https://media.bioworkflows.com/bioworkflows/public_preview/0427548c3d2793ad7c678c3d0ae7b4d42f5a83f03b324149205546fd86f6b6e8.jpg)
ATAC-seq snakemake pipeline
source: http://www.the-scientist.com/?articles.view/articleNo/44772/title/Reveling-in-the-Revealed/ https://www.biostars.org/...
![pyflow-rnaseq](https://media.bioworkflows.com/bioworkflows/public_preview/88cb5e4487296b82d57088487a14e8b60d61a131ad56f2ddedff38fe8e601de6.jpg)
RNAseq pipeline based on snakemake
If you use this pipeline, please cite:
If inputs are fastq files:
The output folder will be suffixed by _fq
I...
![pyflow-scatacseq](https://media.bioworkflows.com/bioworkflows/public_preview/a360df3bc85b86f650820edbe03976da1d8bd91d03f3a54f9d714760103e7f86.jpg)
![cuttag-pipeline](https://media.bioworkflows.com/bioworkflows/public_preview/07a6935d8d1643b03df56b67ca4018640c79988e4375325b5496367fcf47a888.jpg)
Pipeline for Cut&Tag analysis
Snakemake pipeline for Cut&Tag analysis
# cd into a project directory
# type the following to get a copy of the pipeline
git ...
![snakemake_chipseq_pe](https://media.bioworkflows.com/bioworkflows/public_preview/dc6f8ed84efe4ad2c0d9b8b10990b1a3826fa2007d2bbe1fd23e1396346471b9.jpg)
Pipeline for the analysis of PE ChIP-seq data
Snakemake pipeline made for reproducible analysis of paired-end Illumina ChIP-seq data. The desired output of this pipelin...
![atacseq_pipeline](https://media.bioworkflows.com/bioworkflows/public_preview/ce97ee90f2bcd3ed2262f7f9df96b2cb5d0f314720fe6793f9cc775923cc0362.jpg)
Ultimate ATAC-seq Data Processing & Analysis Pipeline
From r A w (unaligned) BAM files to normali Z ed counts. A Snakemake implementation of the BSF's
ATAC-seq Data ...
![bcd_nano_cutntag](https://media.bioworkflows.com/bioworkflows/public_preview/c081a78c62b77bc4d447e6bcb2c1f49a8754117987cc475b7c3fcac1dc088320.jpg)
![genome_tracks](https://media.bioworkflows.com/bioworkflows/public_preview/059b614f53be70a45cbff456a0094e0467a4db8c886d45c4235dc57e6d6a7fb0.jpg)
A Snakemake workflow for easy visualization of genome browser tracks of aligned BAM files powered by the wrapper gtracks for the package pyGenomeTracks.
A Snakemake workflow for easy visualization of genome browser tracks of aligned BAM files (e.g., RNA-seq, ATAC-seq,...) p...
![modr](https://media.bioworkflows.com/bioworkflows/public_preview/584c5d66c865c5fcdda103490cd2e668db4b31b135b732ea222537ddd0e5ceaf.jpg)
An awesome Oxford Nanopore Pipeline for direct RNA-sequencing
An Oxford Nanopore direct RNA-sequencing Pipeline
This is the home of the pipeline, modr. Its long-term goals: to ac...
![rnaseq_workflow](https://media.bioworkflows.com/bioworkflows/public_preview/30178310f45f30da93cce9b120e945ce51aeaa329b11dabb98000e934f3a4dbe.jpg)
![genrich_compare](https://media.bioworkflows.com/bioworkflows/public_preview/dc106d33dd374868817f5bc818a9759c008aa83de4435cddd843f1db8c240e68.jpg)
snakemake workflow comparing Genrich and MACS2
snakemake workflow comparing Genrich and MACS2
bwa/0.7.15 for aligning the reads.
Genrich
git clone the r...