All Published Workflows
12 workflows that have been reviewed and published
Meta-pipeline to identify transposable element insertions using next generation sequencing data
# INSTALL (Requires Conda and Mamba to be installed)
git clone [email protected]:bergmanlab/mcclintock.git
cd mcclintock
mamba e...
mapping pipeline for ancient DNA
Mapache ([maˈpa.t͡ʃe]) is a lightweight mapping pipeline for ancient DNA using the workflow manager Snakemake . Visit ...
Snakemake workflow to download and/or align reads to targets and produce useful outputs.
A Snakemake workflow to download/align reads to targets and produce useful outputs. With hiss, you can:
Download reads fo...
Barcode Mapping and Read Extraction Workflow with bcmap
Maps barcodes to a reference genome and returns genomic windows from which the barcoded reads most likely originate. Each win...
RNA-seq paired-end Workflow
The workflow needs a list of dataset pairs of fastqsanger.
As well as a gtf file with genes
Optional, but recommen...
RNA-seq single-read Pipeline
The workflow needs a list of datasets of fastqsanger.
As well as a gtf file with genes
Optional, but recommended: ...
ChIP-seq paired-end Pipeline
ChIP-seq paired-end Workflow
The workflow needs a single input which is a list of dataset pairs of fastqsanger.
adapt...
BridgeDb workflow: Gene HGNC name to Ensembl identifier
This tutorial explains how to use the BridgeDb identifier mapping service to translate HGNC names to Ensembl identifiers. Thi...
eQTL-Catalogue/qtlmap
eQTL-Catalogue/qtlmap
Portable eQTL analysis and statistical fine mapping workflow used by the eQTL Catalogue
eQTL-Cata...
Preparing a data set for Deep Learning from zipped ABR raw data files
This notebook is about pre-processing the Auditory Brainstem Response (ABR) raw data files provided by Ingham et. al to c...
SPARQL query (in a file) on graph database
The demos of the FAIRness (e.g. digital resources automatically found and reused by machines) for the WP6 of the EU Horizo...
