1. About TF-Prioritizer

This pipeline gives you a full analysis of nfcore chromatine accessibility peak data (ChIP-Seq, ATAC-Seq or DNAse-Seq) and nfcore RNA-seq count data. It performs DESeq2, TEPIC and DYNAMITE including all preprocessing and postprocessing steps necessary to transform the data. It also gives you plots for deep analysis of the data. The general workflow is sketched in the images below:

Graphical abstract:

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Snakemake workflow: Reconstructing raw tomography data

A Snakemake worfklow for tomographically reconstructing raw data using tomopy.

Installation

First download this repo and navigate to it

git clone https://codebase.helmholtz.cloud/gernha62/reconstructing-raw-tomography-data.git 

cd /path/to/repo 

(Optional) Download the example folder with:

wget -m -np https://doi2.psi.ch/datasets/das/work/p15/p15869/compression/MI04_02/tif
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TronFlow BAM preprocessing pipeline

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TronFlow alignment pipeline

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CoVigator pipeline: variant detection pipeline for Sars-CoV-2

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Github: https://github.com/Lcornet/GENERA

BCCM GEN-ERA tools repository

Please visit the wiki for tutorials and access to the tools: https://github.com/Lcornet/GENERA/wiki

NEWS

Mantis is now installed in a singularity container for the Metabolic workflow (install is no longer necessary).

Information about the GEN-ERA project

Please visit https://bccm.belspo.be/content/bccm-collections-genomic-era

Publications

1. ToRQuEMaDA: tool for retrieving queried Eubacteria, metadata and dereplicating ...

The Regulatory Mendelian Mutation (ReMM) score was created for relevance prediction of non-coding variations (SNVs and small InDels) in the human genome (GRCh37) in terms of Mendelian diseases. This project updates the ReMM score for the genome build GRCh38 and combines GRCh37 and GRCh38 into one workflow.

Pre-requirements

Conda

We use Conda as software and dependency management tool. Conda installation guidelines can be found here:

https://conda.io/projects/conda/en/latest/user-guide/install/index.html ...

RNAseq workflow UMG: Here we introduce a scientific workflow implementing several open-source software executed by Galaxy parallel scripting language in an high-performance computing environment. We have applied the workflow to a single-cardiomyocyte RNA-seq data retrieved from Gene Expression Omnibus database. The workflow allows for the analysis (alignment, QC, sort and count reads, statistics generation) of raw RNA-seq data and seamless integration of differential expression results into a ...

RNA-seq Scientific Workflow

Workflow for RNA sequencing using the Parallel Scripting Library - Parsl.

Reference: Cruz, L., Coelho, M., Terra, R., Carvalho, D., Gadelha, L., Osthoff, C., & Ocaña, K. (2021). Workflows Científicos de RNA-Seq em Ambientes Distribuídos de Alto Desempenho: Otimização de Desempenho e Análises de Dados de Expressão Diferencial de Genes. In Anais do XV Brazilian e-Science Workshop, p. 57-64. Porto Alegre: SBC. DOI: https://doi.org/10.5753/bresci.2021.15789 ...