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This package contains the following programs: bamcollate2, bammarkduplicates, bammaskflags, bamrecompress, bamsort, bamtofastq.
This package contains a set of common Perl utilities for generating consistent Vcf headers. It primarily exists to prevent code duplication between some other projects.
MCView creates a Shiny app facilitating interactive exploration and annotation of Metacell models.
SeqAn is a C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. It contains algorithms and data structures for string representation and their manipulation, online and indexed string search, efficient I/O of bioinformatics file formats, sequence alignment, and more.
FastQC aims to provide a QC report which can spot problems which originate either in the sequencer or in the starting library material. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files.
The CodeMin minimization library provides a set of lightweight minimization functions originally developed for the CodeAxe phylogenetic analysis package.
This package provides in uncompressed version of the gnomAD structural variant sites.
This package provides a subset of the Regulatory Sequence Analysis Tools (RSAT).
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.
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.
Wannier90 is a code for generating maximally-localized Wannier functions and using them to compute advanced electronic properties of materials with high efficiency and accuracy. Many electronic structure codes have an interface to Wannier90, and there are several post-processing codes that use the output of Wannier90 for further analysis and calculation.
libxc, a library of exchange-correlation functionals for density-functional theory, aims to provide a portable, well tested and reliable set of exchange and correlation functionals that can be used by a variety of programs.
This package provides Python bindings for the spglib library, used for crystal symmetry search.
PLUMED is a library that provides a wide range of different methods, which include: enhanced-sampling algorithms, free-energy methods, tools to analyze the vast amounts of data produced by molecular dynamics (MD) simulations. These techniques can be used in combination with a large toolbox of collective variables that describe complex processes in physics, chemistry, material science, and biology.
This package provides a module to obtain and visualize k-vector coefficients and obtain band paths in the Brillouin zone of crystal structures.
libMBD implements the many-body dispersion (MBD) method in several programming languages and frameworks (Fortran, C, Python C bindings, Python/Numpy, Python/Tensorflow).
Quantum ESPRESSO is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.
PLUMED is a library that provides a wide range of different methods, which include: enhanced-sampling algorithms, free-energy methods, tools to analyze the vast amounts of data produced by molecular dynamics (MD) simulations. These techniques can be used in combination with a large toolbox of collective variables that describe complex processes in physics, chemistry, material science, and biology.
libxc, a library of exchange-correlation functionals for density-functional theory, aims to provide a portable, well tested and reliable set of exchange and correlation functionals that can be used by a variety of programs.