Bioparser is a C++ header only parsing library for several bioinformatics formats (FASTA/Q, MHAP/PAF/SAM), with support for zlib compressed files.

SHARC is a pipeline for somatic SV calling and filtering from tumor-only Nanopore sequencing data. It performs mapping, SV calling, SV filtering, random forest classification, blacklist filtering and SV prioritization, followed by automated primer design for PCR amplicons of 80-120 bp that are useful to track cancer ctDNA molecules in liquid biopsies.

MetaMaps is tool specifically developed for the analysis of long-read (PacBio/Oxford Nanopore) metagenomic datasets.

Scriabin aims to provide a comprehensive view of cell-cell communication (CCC). It achieves this without requiring subsampling or aggregation.

This package provides a tool to download or view data in the cloud environments of ICGC.

This package provides tools for rapid prokaryotic genome annotation.

hiddenDomains is a suite of programs used to identify significant enrichment of ChIP-seq reads that span large domains, like HK27me3. The input data can be in BAM format, or in a tab-delimited 'reads per bin' format described below. The output is a BED formatted file the lists the enriched domains and their posterior probabilities.

This package provides an implementation of the CaVEMan program. It uses an expectation maximisation approach to calling single base substitutions in paired data. It is designed for use with a compute cluster. Most steps in the program make use of an index parameter. The split step is designed to divide the genome into chunks of adjustable size to optimise for runtime/memory usage requirements.

CAT and BAT are pipelines for the taxonomic classification of long DNA sequences and MAGs of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs. CAT and BAT can be run from intermediate steps if files are formated appropriately.

MCView creates a Shiny app facilitating interactive exploration and annotation of Metacell models.

The carputils framework will be the optimal way to access openCARP for most users. This Python framework was developed to provide the means to easily encode in silico experiments including pre- and postprocessing. carputils will call the openCARP simulator.

This package is designed to help the scientist, engineer, statistician, etc., to construct appropriate experimental designs.

This package is designed to help the scientist, engineer, statistician, etc., to construct appropriate experimental designs.

BLT is a streamlined CMake-based foundation for Building, Linking and Testing large-scale high performance computing (HPC) application.

This package provides bsc and libbsc, a program and a library for lossless, block-sorting data compression. bsc is a high performance file compressor based on lossless, block-sorting data compression algorithms. libbsc is a library based on bsc, it uses the same algorithms as bsc and enables you to compress memory blocks.

zfp is a compressed number format for multi-dimensional arrays. zfp provides compressed-array classes (e.g., for in-memory storage) and high-speed, parallel data compression (e.g., for offline storage). zfp supports both lossy and lossless compression and fine-grained user control over accuracy and storage size.

PDI supports loose coupling of simulation codes with data handling the simulation code is annotated in a library-agnostic way, libraries are used from the specification tree.

RAJA offers portable, parallel loop execution by providing building blocks that extend the generally-accepted parallel for idiom. RAJA relies on standard C++14 features.

CAMP collects a variety of macros and metaprogramming facilities for C++ projects. It's in the direction of projects like metal (a major influence) but with a focus on wide compiler compatibility across HPC-oriented systems.

Decl'HDF5 plugin enables one to read and write data from HDF5 files in a declarative way. Decl'HDF5 does not support the full HDF5 feature set but offers a simple declarative interface to access a large subset of it for the PDI library.

PDI supports loose coupling of simulation codes with data handling the simulation code is annotated in a library-agnostic way, libraries are used from the specification tree.

DDC, is a C++-17 library that aims to offer to the C++/MPI world an equivalent to the xarray.DataArray/dask.Array python environment. Where these two libraries are based on numpy, DDC relies on Kokkos and mdspan to offer CPU/GPU performance-portable multi-dimensional arrays and iterators.