The eiR package provides utilities for accelerated structure similarity searching of very large small molecule data sets using an embedding and indexing approach.

Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data. Analysis of alternative splicing and isoform switches with predicted functional consequences (e.g. gain/loss of protein domains etc.) from quantification of all types of RNASeq by tools such as Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc.

The package enables a simple unified interface to several annotation packages each of which has its own schema by taking advantage of the fact that each of these packages implements a select methods.

A Python package to interface with the ECMWF CADS API.

The Trilinos package Galeri contains a suite of utilities and classes to generate a variety of (distributed) linear systems. Galeri's functionalities are very close to that of the MATLAB's gallery() function. Several well-known finite element and finite difference matrices can be generated using only a few simple code lines.

IFPACK provides a suite of object-oriented algebraic preconditioners for the solution of preconditioned iterative solvers. IFPACK constructors expect an Epetra_RowMatrix object for construction. IFPACK is part of the Trilinos Solver Project and IFPACK object interact well with other Trilinos classes. In particular, IFPACK can be used as a preconditioner for AztecOO.