BamM is a C library, wrapped in Python, to efficiently generate and parse BAM files, specifically for the analysis of metagenomic data. For instance, it implements several methods to assess contig-wise read coverage.

COUGER can be applied to any two sets of genomic regions bound by paralogous TFs (e.g., regions derived from ChIP-seq experiments) to identify putative co-factors that provide specificity to each TF. The framework determines the genomic targets uniquely-bound by each TF, and identifies a small set of co-factors that best explain the in vivo binding differences between the two TFs.

COUGER uses classification algorithms (support vector machines and random forests) with features that reflect the DNA binding specificities of putative co-factors. The features are generated either from high-throughput TF-DNA binding data (from protein binding microarray experiments), or from large collections of DNA motifs.

Samtools implements various utilities for post-processing nucleotide sequence alignments in the SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction with bcftools), and a simple alignment viewer.

QTLtools is a tool set for molecular QTL discovery and analysis. It allows going from the raw genetic sequence data to collection of molecular Quantitative Trait Loci (QTLs) in few easy-to-perform steps.

Samtools implements various utilities for post-processing nucleotide sequence alignments in the SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction with bcftools), and a simple alignment viewer.

HTSlib is a C library for reading/writing high-throughput sequencing data. It also provides the bgzip, htsfile, and tabix utilities.

BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.

HTSlib is a C library for reading/writing high-throughput sequencing data. It also provides the bgzip, htsfile, and tabix utilities.

HTSlib is a C library for reading/writing high-throughput sequencing data. It also provides the bgzip, htsfile, and tabix utilities.

A collection of libraries intended to be widely useful, and usable across a broad spectrum of applications.

A collection of libraries intended to be widely useful, and usable across a broad spectrum of applications.

A collection of libraries intended to be widely useful, and usable across a broad spectrum of applications.

A collection of libraries intended to be widely useful, and usable across a broad spectrum of applications.

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 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.

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.

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.

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).

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.