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  • ACESeq ACEseq is a method to detect somatic copy number variations from matching tumor/control WGS data pairs. In addition to total ...
  • Alfred Alfred is a comprehensive NGS alignment quality control method that supports commonly used QC metrics, RNA and DNA feature counting ...
  • biomaRt Provides an R interface to BioMart services. In particular this is the most widely used programmatic access route to query ...
  • BUTLER Provides an R interface to BioMart services. In particular this is the most widely used programmatic access route to query ...
  • CESAM Enables the discovery of oncogene activation events mediated by enhancer hijacking, via pan-cancer analyses. Homepage https://bitbucket.org/weischen/cesam Contact Jan Korbel (korbel (at) embl (dot) de) Relevant ...
  • DELLY Delly is a structural variant detection method for the discovery of germline and somatic genomic rearrangements. Delly can detect deletions, ...
  • DESeq2 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, ...
  • DEXSeq DEXSeq is an extension of DESeq for the analysis of alternative exon usage. DESeq2 is an R/Bioconductor package for differential ...
  • Gear Gear is a genome analysis web server hosting applications for molecular biologists to analyze Sanger traces, design PCR primers and ...
  • IHW Independent hypothesis weighting (IHW) is a multiple testing procedure that increases power compared to commonly used alternatives for false discovery ...
  • Indel calling pipeline The indel pipeline detects high confidence indels (1-20 bp). The results are presented in an extensively annotated VCF file. The ...
  • IONiseR IONiseR provides tools for the quality assessment of Oxford Nanopore MinION data. It extracts summary statistics from a set of ...
  • Mechismo Mechismo is a tool that allows rapid predictions of how genetic variants impact on biomolecular function. This is done by ...
  • OTP The “One Touch Pipeline” is a comprehensive framework for NGS project organization and processing. The application provides support in ...
  • Pan-Cancer alignment workflow The alignment workflow produces aligned bam files from fastq files. The user can choose between different versions of bwa. The ...
  • rhdf5 & Rhdf5lib The rhdf5 and Rhdf5lib packages combine to provide an interface between HDF5 and R. The HDF5 file format provides the ...
  • RNA-seq end-to-end workflow End-to-end gene-level RNA-Seq differential expression workflow using Bioconductor packages. Starting from the FASTQ files, these are aligned to the reference ...
  • Roddy Roddy is a framework for large scale NGS processing pipelines on Petabyte scale. It is used for the management of ...
  • SIDER SIDER is a web-based resource that contains information on marketed medicines and their recorded adverse drug reactions. This information is ...
  • SMART SMART (Simple Modular Architecture Research Tool) is a web resource providing simple identification and extensive annotation of protein domains via ...
  • SNV calling pipeline The SNV pipeline creates a set of high confidence somatic SNVs. The pipeline takes a tumor and matched control bam ...
  • STITCH STITCH is a web-based resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other ...
  • STRING STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) is a database of known and predicted protein interactions in the ...
  • TPP Detecting the binding partners of a drug is one of the biggest challenges in drug research. Thermal Proteome Profiling (TPP) ...
  • YAPSA This package provides functions and routines for a supervised analysis of somatic signatures. In particular, functions to perform a signature ...