ACEseq is a method to detect somatic copy number variations from matching tumor/control WGS data pairs. In addition to total copy numbers it provides allele-specific copy numbers as well as ploidy and tumor cell content estimates for the tumor sample.

Contact

Dr. Matthias Schlesner
Kortine Kleinheinz (This email address is being protected from spambots. You need JavaScript enabled to view it.)


 

Alfred is a comprehensive NGS alignment quality control method that supports commonly used QC metrics, RNA and DNA feature counting and flexible feature annotation.

Funding: 

Neither development nor maintenance funded by de.NBI.

Homepage: 

https://github.com/tobiasrausch/alfred

Bioconda: 

https://bioconda.github.io/recipes/alfred/README.html

Contact:

This email address is being protected from spambots. You need JavaScript enabled to view it.


Provides an R interface to BioMart services. In particular this is the most widely used programmatic access route to query EMBL-EBI’s Ensembl database.

Homepage

https://bioconductor.org/packages/biomaRt/

Relevant Publications

Contact

Wolfgang Huber (This email address is being protected from spambots. You need JavaScript enabled to view it.)
Mike Smith


 

Framework for the cloud orchestration of genomics workflows.

Homepage

https://github.com/llevar/butler

Contact

Sergej Iakhnin (This email address is being protected from spambots. You need JavaScript enabled to view it.)


 

Enables the discovery of oncogene activation events mediated by enhancer hijacking, via pan-cancer analyses.

Homepage:

https://bitbucket.org/weischen/cesam

Relevant papers:

Pan-cancer analysis of somatic copy-number alterations implicates IRS4 and IGF2 in enhancer hijacking.

Contact

Jan Korbel (This email address is being protected from spambots. You need JavaScript enabled to view it.)

Delly is a structural variant detection method for the discovery of germline and somatic genomic rearrangements. Delly can detect deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data.

Funding:

Neither development nor maintenance funded by de.NBI.

Homepage: 

https://github.com/dellytools/delly

BioTools: 

https://bio.tools/delly2

Bioconda: 

https://bioconda.github.io/recipes/delly/README.html

Contact: 

This email address is being protected from spambots. You need JavaScript enabled to view it.

DESeq2 is an R/Bioconductor package for differential expression analysis of high-throughput sequencing assays (incl. RNA-seq, ChIP-Seq, 4C-Seq, ribosome profiling, CLIP, metagenomics, HT-CRISPR screens) based on the Gamma-Poisson distribution.

Homepage

http://bioconductor.org/packages/release/bioc/html/DESeq2.html

Contact

Wolfgang Huber (This email address is being protected from spambots. You need JavaScript enabled to view it.)
Mike Smith

DEXSeq is an extension of DESeq for the analysis of alternative exon usage. DESeq2 is an R/Bioconductor package for differential expression analysis of high-throughput sequencing assays (incl. RNA-seq, ChIP-Seq, 4C-Seq, ribosome profiling, CLIP, metagenomics, HT-CRISPR screens) based on the Gamma-Poisson distribution.

Homepage

http://bioconductor.org/packages/DEXseq/

Contact

Wolfgang Huber (This email address is being protected from spambots. You need JavaScript enabled to view it.)
Mike Smith

Gear is a genome analysis web server hosting applications for molecular biologists to analyze Sanger traces, design PCR primers and perform DNA sequence analyses.

Homepage: 

https://gear.embl.de

Contact: 

This email address is being protected from spambots. You need JavaScript enabled to view it.


 

Independent hypothesis weighting (IHW) is a multiple testing procedure that increases power compared to commonly used alternatives for false discovery rate (FDR) control by assigning data-driven weights to each hypothesis.  The IHW software package provide a mechanism that allows the methodology to be applied to many different data types.

Homepage

http://bioconductor.org/packages/release/bioc/html/IHW.html

Contact

Wolfgang Huber (This email address is being protected from spambots. You need JavaScript enabled to view it.)

The indel pipeline detects high confidence indels (1-20 bp). The results are presented in an extensively annotated VCF file. The input of the pipeline are the aligned tumor and control bam files. To enable a fast quality assessment of functionally indels screen shots are taken of exotic high confidence indels.

Contact

Dr. Matthias Schlesner

IONiseR provides tools for the quality assessment of Oxford Nanopore MinION data. It extracts summary statistics from a set of fast5 files and can be used either before or after base calling. In addition to standard summaries of the read-types produced, it provides a number of plots for visualising metrics relative to experiment run time or spatially over the surface of a flowcell.

Homepage

http://bioconductor.org/packages/release/bioc/html/IONiseR.html

Contact

Mike Smith

Mechismo is a tool that allows rapid predictions of how genetic variants impact on biomolecular function. This is done by a pre-computed collection of protein-protein, protein-DNA/RNA, protein-chemical interactions of known three-dimensional structure mapped to proteomes from major model organisms.  Users can input any number of variants to get a ranked list of genes and specific positions that have a functional impact on biomolecular interactions.

Homepage:

http://mechismo.russelllab.org/

Contact:

Prof. Dr. Rob Russell

The "One Touch Pipeline" is a comprehensive framework for NGS project  organization and processing. The application provides support in all steps of this process, including data transfer from temporary to final  storage, execution of data quality monitoring programs, alignment of  reads to the reference genome and variant calling. It allows full  automatization, extended project administration, and full processing control for operators.

Homepage

https://otp.dkfz.de/otp/

Contact

This email address is being protected from spambots. You need JavaScript enabled to view it.
Jürgen Eils (This email address is being protected from spambots. You need JavaScript enabled to view it.)

The alignment workflow produces aligned bam files from fastq files. The user can choose between different versions of bwa. The default settings of the workflow are implemented after the ICGC PanCancer workflow. The pipeline also produces a rich set of quality values as well as coverage plots for each genome individually and combined ones if a tumor normal pair is processed.

Contact

Dr. Matthias Schlesner

The rhdf5 and Rhdf5lib packages combine to provide an interface between HDF5 and R.   The HDF5 file format provides the ability to store and access very large and/or complex datasets and a wide variety of metadata on mass storage (disk) in a completely portable manner. The rhdf5 package is thus suited for the exchange of large and/or complex datasets between R and other software package, and for letting R applications work on datasets that are larger than the available RAM. 

In particular HDF5 is being used to address the rapid growth in the size of single-cell datasets, and rhdf5 is a cornerstone to many existing analysis tools.

Funding: 

Continuing development, support, and maintenance funded by de.NBI.

Homepage: 

https://www.bioconductor.org/packages/rhdf5/

https://www.bioconductor.org/packages/Rhdf5lib/

Development: 

https://github.com/grimbough/rhdf5

https://github.com/grimbough/Rhdf5lib

Contact:

Mike Smith


End-to-end gene-level RNA-Seq differential expression workflow using Bioconductor packages. Starting from the FASTQ files, these are aligned to the reference genome, and a count matrix which tallies the number of RNA-seq reads/fragments within each gene for each sample is prepared. Performance of exploratory data analysis (EDA) for quality assessment and exploration of the relationship between samples, performance of differential gene expression analysis, and visual exploration of the results.

Homepage

http://www.bioconductor.org/help/workflows/rnaseqGene/

Contact

Wolfgang Huber (This email address is being protected from spambots. You need JavaScript enabled to view it.)
Mike Smith

Roddy is a framework for large scale NGS processing  pipelines on Petabyte scale. It is used for the management of workflows in the Pan-Cancer Analysis of Whole Genomes (PCAWG) project.

Homepage

https://github.com/eilslabs/Roddy/wiki

https://github.com/eilslabs/Roddy/wiki/Example-workflow

Contact

Dr. Matthias Schlesner
Michael Heinold

SIDER is a web-based resource that contains information on marketed medicines and their recorded adverse drug reactions. This information is extracted from public documents and package inserts. SIDER makes available side effect frequency, drug and side effect classifications as well as links to further information, for example drug–target relations. It currently covers associations between 5,868 side effects and 1,430 drugs.

Homepage

http://sideeffects.embl.de/

Contact

Dr. Georg Zeller

SMART (Simple Modular Architecture Research Tool) is a web resource providing simple identification and extensive annotation of protein domains via sequence homology searches. It contains manually curated models for more than 1,200 protein domains. In its ‘Genomic’ mode, it annotates proteins from completely sequenced genomes of 2,031 species as a basis for their functional annotation. It provides flexible tools to visually explore protein domain architectures across sequences and organisms.

Homepage

http://smart.embl.de/

Contact

Dr. Georg Zeller

The SNV pipeline creates a set of high confidence somatic SNVs. The pipeline takes a tumor and matched control bam file as input and returns a highly annotated VCF file. In addition the workflow produces plots that help to interpret both, the sample quality (e.g. if the sample is contaminated) as well as biology (e.g. if the sample shows kataegis).

Contact

Dr. Matthias Schlesner

STITCH is a web-based resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature. STITCH contains interactions between 300,000 small molecules and 2.6 million proteins from 1133 organisms.

Homepage

http://stitch.embl.de/

Contact

Dr. Georg Zeller

STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) is a database of known and predicted protein interactions in the form of direct physical or indirect functional associations, which currently cover 9,643,763 proteins from 2,031 organisms. Interaction data are derived from high-throughput experiments, genomic context, (conserved) coexpression, and the scientific literature. STRING quantitatively integrates interaction data from these sources and transfers information between organisms where applicable.

Homepage

http://string.embl.de/

Contact

Dr. Georg Zeller

Detecting the binding partners of a drug is one of the biggest challenges in drug research. Thermal Proteome Profiling (TPP) addresses this question by combining the cellular thermal shift assay concept with mass spectrometry based proteome-wide protein quantitation.  The analysis of such  experiments requires several data analytic and statistical modeling steps.   The package TPP facilitates this process by providing executable workflows that conduct all necessary steps to perform an analysis.

Homepage

http://bioconductor.org/packages/release/bioc/html/TPP.html

Contact

Wolfgang Huber (This email address is being protected from spambots. You need JavaScript enabled to view it.)

This package provides functions and routines for a supervised analysis of somatic signatures. In particular, functions to perform a signature analysis with known signatures (LCD = linear combination decomposition) and a signature analysis on stratified mutational catalogue (SMC = stratify mutational catalogue) are provided.

Homepage

https://bioconductor.org/packages/release/bioc/html/YAPSA.html

Relevant Publications

Integration of genomics and histology revises diagnosis and enables effective therapy of refractory cancer of unknown primary with PDL1 amplification. (2016) Gröschel S, Bommer M, Hutter B, Budczies J, Bonekamp D, Heining C, Horak P, Fröhlich M, Uhrig S, Huebschmann D, Geörg C, Richter D, Pfarr N, Pfütze K, Wolf S, Schirmacher P, Jäger D, von Kalle C, Brors B, Glimm H, Weichert W, Stenzinger A, Fröhling S Cold Spring Harb Mol Case Stud, 2, 6, a001180

Mutant KIT as Imatinib-Sensitive Target in Metastatic Sinonasal Carcinoma. (2016) Dieter SM, Heining C, Agaimy A, Huebschmann D, Bonekamp D, Hutter B, Ehrenberg KR, Fröhlich M, Schlesner M, Scholl C, Schlemmer HP, Wolf S, Mavratzas A, Jung CS, Gröschel S, Kalle CV, Eils R, Brors B, Penzel R, Kriegsmann M, Reuss DE, Schirmacher P, Ann Oncol, pii: mdw446.

Contact

Daniel Huebschmann (This email address is being protected from spambots. You need JavaScript enabled to view it.)

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