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.

Easel is an ANSI C code library developed by the Eddy/Rivas laboratory at Harvard. Easel supports our work on computational analysis of biological sequences using probabilistic models. Easel is used by HMMER, the profile hidden Markov model software that underlies several protein and DNA sequence family databases such as Pfam, and by Infernal, the profile stochastic context-free grammar software that underlies the Rfam RNA family database. Easel aims to make similar applications more robust and easier to develop, by providing a set of reusable, documented, and well-tested functions.

This package computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecaller.

Mellon is a non-parametric cell-state density estimator based on a nearest-neighbors-distance distribution. It uses a sparse gaussian process to produce a differntiable density function that can be evaluated out of sample.

The goal of NicheNet is to study intercellular communication from a computational perspective. NicheNet uses human or mouse gene expression data of interacting cells as input and combines this with a prior model that integrates existing knowledge on ligand-to-target signaling paths. This allows to predict ligand-receptor interactions that might drive gene expression changes in cells of interest.

The CodeMin minimization library provides a set of lightweight minimization functions originally developed for the CodeAxe phylogenetic analysis package.

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.

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

This package provides a Python API for the TREXIO library, which enables interactive calls to the library. It facilitates the development of interfaces between different codes and can be used to convert data from one input/output file format into another.

Atomes is a toolbox developed to analyze, to visualize and to create/edit three-dimensional atomistic models. It offers a workspace that allows users to have many projects opened simultaneously.

scikit-matter is a toolbox of methods developed in the computational chemical and materials science community, following the scikit-learn API and coding guidelines to promote usability and interoperability with existing workflows.

This package provides Python bindings for the spglib library, used for crystal symmetry search.

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.

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.

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.

TREXIO is an open-source file format and library developed for the storage and manipulation of data produced by quantum chemistry calculations. It is designed with the goal of providing a reliable and efficient method of storing and exchanging wave function parameters and matrix elements. The library consists of a front-end implemented in the C programming language and two different back-ends: a text back-end and a binary back-end utilizing the HDF5 library which enables fast read and write operations.

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.

libMBD implements the many-body dispersion (MBD) method in several programming languages and frameworks (Fortran, C, Python C bindings, Python/Numpy, Python/Tensorflow).

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.