Our software

robust proportion analysis for single cell resolution data

Scanpro

Scanpro is a modular tool for proportion analysis, seamlessly integrating into widely accepted frameworks in the python environment. Scanpro is fast, accurate, support datasets without replicates, and is intended to be used by bioinformatics experts and beginners. read more

A framework to streamline single cell analysis.

SC-Framework

The SC-Framework is comprised of a python package and a collection of jupyter notebooks to enable a concise and reproducible method to do single cell analysis. read more

Improving quality control of single-cell ATAC-seq data

PeakQC

A novel algorithm based on a single wavelet transform like convolution to automate quality assessment for single-cell ATAC-seq data. read more

Nucleosome Positioning - NucleoDetective.

NucleoDetective

NucleoDetective is a tool to predict nucleosome positions using ATAC-seq data and to compare the found patterns across different conditions. read more

Pipelines to process bulk high throughput sequencing data.

Bulk Pipelines

Bulk RNA/ATAC/ChIP-Seq are analyzed via in-house software pipelines. read more

Find single nucleotide polymorphisms for precise ORF disruption

WobbleDORF

WobbleDORF is an modular structured command line tool to find single nucleotide polymorphisms, that would disrupt an open reading frame. Main Feature is the frame specific preservation via wobble bases. read more

Design and implementation of a tool to identify genetic directional dependencies.

Genetic directional dependencies

Prediction of combinatorial phenotypes in which the order of mutations direct the phenotype from CRISPR pertubation screens. read more

A R based package for gRNA design

multicrispr²

multicrispr² is a R based pacakge for designing gRNAs with the special feature of designing gRNA pairs intended for genomic excision. read more

A complete framework for performing TF co-occurence and TF grammar analysis

TF-COMB

TF-COMB (Transcription Factor Co-Occurrence using Market Basket analysis) is a framework of methods for investigating transcription factor co-occurrence and and grammar of TF binding. read more

Design and implementation of a tool to manage experimental metadata

FRED

FRED (FaiR Experimental Design) is a program to generate, edit and search metadata in a predefined structure. read more

A pipeline for generation of novel transcription factor motifs

DENIS

DENIS (DE Novo motIf diScovery pipeline) is a pipeline constructing binding motifs for unknown transcription factors from ATAC-seq data read more

A complete framework for performing footprinting analysis on ATAC-seq data

TOBIAS

TOBIAS (Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal) is a framework of tools for investigating transcription factor binding from ATAC-seq signal. read more

MAnaging Computing SErvices on Kubernetes

MACSEK

MACSEK(MAnaging Computing SErvices on Kubernetes) is a framework that provides a computing service on Kubernetes cluster, such as provided by deNBi. It creates a service on the clusters, which allows the upload of files for all kinds of calculation, manages resource allocation on the cluster and provides the download of the results. read more

Iterative & Interactive dashboards

i2dash

Scientific communication and data visualization are important aspects to illustrate complex concepts and results from data analyses. The R package i2dash provides functionality to create customized, web-based dashboards for data presentation, exploration and sharing. i2dash integrates easily into existing data analysis pipelines and can organize scientific findings thematically across different pages and layouts. read more

MAnaging Multiple Projects On Kubernetes

MaMPOK

MaMPOK is an offline Kubernetes management tool. It is intented to use Kubernetes cloud computing at de.NBi. It provides methods to deploy e.g. web apps as containers automatically. It automates file transfers via a S3 object storage, takes care of container images, and keep track of a large number of projects. read more

The tool for MS metadata

MARMoSET

Extracting Mass Spectrometry Metadata from RAW Files is laborious and needs a lot of manual interaction. MARMoSET is intended to automate and arange metadata for various reporting- and journal standards. read more

Visualization of omics data

WIlsON

High-throughput (HT) studies of complex biological systems generate a massive amount of omics data. The results are typically summarized using spreadsheet like file formats. Visualization of this data is a key aspect of both, the analysis and the understanding of biological systems under investigation. While users have many visualization methods and tools to choose from, the challenge is to properly handle these tools and create clear, meaningful, and integrated visualizations based on pre-processed datasets. read more

a tool for Universal RObust Peak Annotation

UROPA

UROPA (Universal RObust Peak Annotator) is a command line based tool, intended for universal genomic range annotation. Based on a configuration file, different target features can be prioritized with multiple integrated queries. These can be sensitive for feature type, distance, strand specificity, feature attributes (e.g. protein_coding) or anchor position relative to the feature. read more

Analysis and visualization of differential methylation in genomic regions

ADMIRE

DNA methylation at cytosine nucleotides constitutes epigenetic gene regulation impacting cellular development and the stage of a disease. Besides whole genome bisulfit sequencing, Illumina HumanMethylationEPIC Assays represent a versatile and cost-effective tool to investigate changes of methylation patterns at CpG sites. ADMIRE is a semi-automatic analysis pipeline and visualization tool for Infinium HumanMethylation450K and Infinium MethylationEpic assays. read more