Our software

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

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

Design and implementation of a tool to manage experimental metadata

MetaTools

MetaTools is a program to store metadata in an organized way and to search it. 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(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

link miRNAs to targets

LimiTT

Our freely available web-based pipeline LimiTT (https://bioinformatics.mpi-bn.mpg.de/) is optimized to determine microRNA-target-interactions (MTIs) with and without species specification. It links miRNAs and/or putative targets with high granularity. The integrated mapping to homologous target identifiers enables the identification of MTIs not only for standard models, but for niche model organisms as well. 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

quantification of microRNAs in niche model organisms

MIRPIPE

We introduce the MIRPIPE application enabling rapid and simple browser-based miRNA homology detection and quantification. MIRPIPE features automatic trimming of raw RNA-Seq reads originating from various sequencing instruments, processing of isomiRs and quantification of detected miRNAs versus public- or user-uploaded reference databases. read more

a comprehensive repository for omics data from the newt Notophthalmus viridescens

Newt-omics

Newt-omics is a transcript-centred database, based on an Expressed Sequence Tag (EST) data set from the newt, covering ~50,000 Sanger sequenced transcripts and a set of high-density microarray data, generated from regenerating hearts. Newt-omics also contains a large set of peptides identified by mass spectrometry, which was used to validate 13,810 ESTs as true protein coding. read more