Click on the headings below to read more.

  • ACESeq

    ACEseq is a method to detect somatic copy number variations from matching tumor/control WGS data pairs.

  • Alfred

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

  • biomaRt

    Provides an R interface to BioMart services.

  • BUTLER

    Framework for the cloud orchestration of genomics workflows.

  • CESAM

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

  • DELLY

    Delly is a structural variant detection method for the discovery of germline and somatic genomic rearrangements.

  • DESeq2

    DESeq2 is an R/Bioconductor package for differential expression analysis of high-throughput sequencing assays based on the Gamma-Poisson distribution.

  • DEXSeq

    DEXSeq is an extension of DESeq2 for the analysis of alternative exon usage.

  • Gear

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

  • IHW

    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.

  • Indel calling pipeline

    The indel pipeline detects high confidence indels (1-20 bp).

  • IONiseR

    IONiseR provides tools for the quality assessment of Oxford Nanopore MinION data.

  • Mechismo

    Mechismo is a tool that allows rapid predictions of how genetic variants impact on biomolecular function.

  • OTP

    The "One Touch Pipeline" is a comprehensive framework for NGS project organization and processing.

  • Pan-Cancer alignment workflow

    The alignment workflow produces aligned bam files from fastq files.

  • rhdf5 & Rhdf5lib

    The rhdf5 and Rhdf5lib packages combine to provide an interface between HDF5 and R.

  • RNA-seq end-to-end workflow

    End-to-end gene-level RNA-Seq differential expression workflow using Bioconductor packages.

  • Roddy

    Roddy is a framework for large scale NGS processing pipelines on Petabyte scale.

  • SIDER

    SIDER is a web-based resource that contains information on marketed medicines and their recorded adverse drug reactions.

  • SMART

    SMART (Simple Modular Architecture Research Tool) is a web resource providing simple identification and extensive annotation of protein domains via sequence homology searches.

  • SNV calling pipeline

    The SNV pipeline creates a set of high confidence somatic SNVs.

  • STITCH

    STITCH is a web-based resource to explore known and predicted interactions of chemicals and proteins.

  • STRING

    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.

  • TPP

    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.

  • YAPSA

    YAPSA provides functions and routines for a supervised analysis of somatic signatures.