Bakefile takes compiler-independent description of build tasks as its input and outputs native makefile(s) such as that of GNU Make, Visual C++ project, etc.

DomainFinder is an interactive program for the determination and characterization of dynamical domains in proteins. It can infer dynamical domains by comparing two protein structures, or from normal mode analysis on a single structure. The software is currently not actively maintained and works only with Python 2 and NumPy < 1.9.

nMOLDYN is an interactive analysis program for Molecular Dynamics simulations. It is especially designed for the computation and decomposition of neutron scattering spectra, but also computes other quantities. The software is currently not actively maintained and works only with Python 2 and NumPy < 1.9.

This package is an R package designed for QC, analysis, and exploration of single cell RNA-seq data. It easily enables widely-used analytical techniques, including the identification of highly variable genes, dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering algorithms; density clustering, hierarchical clustering, k-means, and the discovery of differentially expressed genes and markers.

This package defines S4 classes for single-cell genomic data and associated information, such as dimensionality reduction embeddings, nearest-neighbor graphs, and spatially-resolved coordinates. It provides data access methods and R-native hooks to ensure the Seurat object is familiar to other R users.

Graphviz is a graph visualization tool suite. Graph visualization is a way of representing structural information as diagrams of abstract graphs and networks. It has important applications in networking, bioinformatics, software engineering, database and web design, machine learning, and in visual interfaces for other technical domains.

G-Wrap is a tool and Guile library for generating function wrappers for inter-language calls. It currently only supports generating Guile wrappers for C functions. Given a definition of the types and prototypes for a given C interface, G-Wrap will automatically generate the C code that provides access to that interface and its types from the Scheme level.

Guile-Lib is intended as an accumulation place for pure-scheme Guile modules, allowing for people to cooperate integrating their generic Guile modules into a coherent library. Think "a down-scaled, limited-scope CPAN for Guile". It provides the following modules:

• (apicheck) Describe and verify library programming interfaces.

• (config load) Loading configuration files.

• (container async-queue) A thread-safe message queue.

• (container nodal-tree) A tree consisting of nodes with attributes.

• (container delay-tree) A nodal tree with lazily evaluated fields.

• (debugging assert) Helpful assert macro.

• (debugging time) A simple macro to time the execution of an expression.

• (graph topological-sort) Routines to perform topological sorts.

• (htmlprag) Neil Van Dyke's permissive ("pragmatic") HTML parser.

• (io string) SLIB's IO routines dealing with strings.

• (logging logger) A flexible logging system.

• (logging port-log) A logger that outputs to a port.

• (logging rotating-log) A logger that rotates its output files.

• (match-bind) Nifty and concise regular expression routines.

• (math minima) A golden-section minimum finder.

• (math primes) Functions related to prime numbers and factorization.

• (os process) Spawning processes and capturing their output.

• (scheme documentation) Macros to define different kinds of variables with documentation.

• (scheme kwargs) Defining functions with flexible keyword arguments.

• (search basic) Classic search functions.

• (string completion) Building blocks for tab completion.

• (string soundex) The SOUNDEX string categorization algorithm.

• (string transform) Beyond SRFI-13.

• (string wrap) A versatile string formatter.

• (term ansi-color) Generate ANSI color escape sequences.

• (unit-test) A JUnit-style unit testing framework.

Vinci implements a number of volume computation algorithms for convex polytopes in arbitrary dimension. The polytopes can be given by their V-representation (as the convex hull of a finite number of vertices), by their H-representation (as the bounded intersection of a finite number of halfspaces) or by their double description with both representations.

The GNU Scientific Library is a library for numerical analysis in C and C++. It includes a wide range of mathematical routines, with over 1000 functions in total. Subject areas covered by the library include: differential equations, linear algebra, Fast Fourier Transforms and random numbers.

The C code of lrslib implements the reverse search algorithm for vertex enumeration and convex hull problems. Its input file format is compatible with cddlib. All computations are done exactly in either multiple precision or fixed integer arithmetic. Output is not stored in memory, so even problems with very large output sizes can sometimes be solved.

Primal-dual, or pd in short, implements an algorithm for computing the vertex representation from the facet representation of a convex polytope, and vice versa. It uses one direction as an oracle for the other one, so it is meant to work well when other algorithms face a difficult direction (and should be avoided for the easy direction).

Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull. It handles roundoff errors from floating point arithmetic. It computes volumes, surface areas, and approximations to the convex hull.

Qhull does not support triangulation of non-convex surfaces, mesh generation of non-convex objects, medium-sized inputs in 9-D and higher, alpha shapes, weighted Voronoi diagrams, Voronoi volumes, or constrained Delaunay triangulations.

Perl is a general-purpose programming language originally developed for text manipulation and now used for a wide range of tasks including system administration, web development, network programming, GUI development, and more.

Perl is a general-purpose programming language originally developed for text manipulation and now used for a wide range of tasks including system administration, web development, network programming, GUI development, and more.

This Python library allows reading and writing to the Excel XLSX, XLSM, XLTX and XLTM file formats that are defined by the Office Open XML (OOXML) standard.

The pyparsing module is an alternative approach to creating and executing simple grammars, vs. the traditional lex/yacc approach, or the use of regular expressions. The pyparsing module provides a library of classes that client code uses to construct the grammar directly in Python code.

This package provides an implementation of importlib.resources for older versions of Python.

Unittest2 is a replacement for the unittest module in the Python standard library.

The dateutil module provides powerful extensions to the standard datetime module, available in Python 2.3+.

Python's built-in itertools module implements a number of iterator building blocks inspired by constructs from APL, Haskell, and SML. more-itertools includes additional building blocks for working with iterables.

This package provides a Python library intended for use in automated tests. One difficulty when testing software is that the code under test might need to read or write to files in the local file system. If the file system is not set up in just the right way, it might cause a spurious error during the test. The pyfakefs library provides a solution to problems like this by mocking file system interactions. In other words, it arranges for the code under test to interact with a fake file system instead of the real file system. The code under test requires no modification to work with pyfakefs.

The goal of pathlib2 is to provide a backport of standard pathlib module which tracks the standard library module, so all the newest features of the standard pathlib can be used also on older Python versions.

Pathlib offers a set of classes to handle file system paths. It offers the following advantages over using string objects:

1. No more cumbersome use of os and os.path functions. Everything can be done easily through operators, attribute accesses, and method calls.

2. Embodies the semantics of different path types. For example, comparing Windows paths ignores casing.

3. Well-defined semantics, eliminating any inconsistencies or ambiguities (forward vs. backward slashes, etc.).

This is a backport of the subprocess standard library module from Python 3.2 and 3.3 for use on Python 2. It includes bugfixes and some new features. On POSIX systems it is guaranteed to be reliable when used in threaded applications. It includes timeout support from Python 3.3 but otherwise matches 3.2’s API.