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

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.

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.

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.

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.

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.

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

This is a collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.

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

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.

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.

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.

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.

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.