Click on the headings below to read more.
ACEseq is a method to detect somatic copy number variations from matching tumor/control WGS data pairs.
Alfred is a comprehensive NGS alignment quality control method that supports commonly used QC metrics, RNA and DNA feature counting and flexible feature annotation.
Provides an R interface to BioMart services.
Framework for the cloud orchestration of genomics workflows.
Enables the discovery of oncogene activation events mediated by enhancer hijacking, via pan-cancer analyses.
Delly is a structural variant detection method for the discovery of germline and somatic genomic rearrangements.
DESeq2 is an R/Bioconductor package for differential expression analysis of high-throughput sequencing assays based on the Gamma-Poisson distribution.
DEXSeq is an extension of DESeq2 for the analysis of alternative exon usage.
Gear is a genome analysis web server hosting applications for molecular biologists to analyze Sanger traces, design PCR primers and perform DNA sequence analyses.
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 provides tools for the quality assessment of Oxford Nanopore MinION data.
Mechismo is a tool that allows rapid predictions of how genetic variants impact on biomolecular function.
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 is a framework for large scale NGS processing pipelines on Petabyte scale.
SIDER is a web-based resource that contains information on marketed medicines and their recorded adverse drug reactions.
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 is a web-based resource to explore known and predicted interactions of chemicals and proteins.
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.
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 provides functions and routines for a supervised analysis of somatic signatures.