The benchmarks are derived from computational fluid dynamics (CFD) applications and consist of five kernels and three pseudo-applications in the original "pencil-and-paper" specification (NPB 1). The benchmark suite has been extended to include new benchmarks for unstructured adaptive meshes, parallel I/O, multi-zone applications, and computational grids. Problem sizes in NPB are predefined and indicated as different classes.

The benchmarks are derived from computational fluid dynamics (CFD) applications and consist of five kernels and three pseudo-applications in the original "pencil-and-paper" specification (NPB 1). The benchmark suite has been extended to include new benchmarks for unstructured adaptive meshes, parallel I/O, multi-zone applications, and computational grids. Problem sizes in NPB are predefined and indicated as different classes.

mpiGraph is a MPI benchmark to generate network bandwidth images.

Create an interactive Shiny-based graphical user interface for exploring data stored in SummarizedExperiment objects, including row- and column-level metadata. The interface supports transmission of selections between plots and tables, code tracking, interactive tours, interactive or programmatic initialization, preservation of app state, and extensibility to new panel types via S4 classes. Special attention is given to single-cell data in a SingleCellExperiment object with visualization of dimensionality reduction results.

This is an R package which interfaces with the OME Bio-Formats Java library to allow reading of proprietary microscopy image data and metadata.

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

This package contains the following programs: bamcollate2, bammarkduplicates, bammaskflags, bamrecompress, bamsort, bamtofastq.

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 provides a subset of the Regulatory Sequence Analysis Tools (RSAT).

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

The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.

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.

This package contains a few simple math function for other Oxford Nanopore processing scripts.

hiddenDomains is a suite of programs used to identify significant enrichment of ChIP-seq reads that span large domains, like HK27me3. The input data can be in BAM format, or in a tab-delimited 'reads per bin' format described below. The output is a BED formatted file the lists the enriched domains and their posterior probabilities.

Bioparser is a C++ header only parsing library for several bioinformatics formats (FASTA/Q, MHAP/PAF/SAM), with support for zlib compressed files.

This module provides code coverage metrics for Perl. Code coverage metrics describe how thoroughly tests exercise code. By using Devel::Cover you can discover areas of code not exercised by your tests and determine which tests to create to increase coverage.

Primer3-py is a Python-abstracted API for the popular Primer3 library. The intention is to provide a simple and reliable interface for automated oligo analysis and design.

Primer3-py also includes bindings for the Primer3 primer design engine if you’d prefer to use an established pipeline. The IO parameters mirror those of the original Primer3, but you don’t have to deal with messy and slow file IO for your automated workflows.

This package is used to apply filtering on raw VCF calls generated using CaVEMan.

This package provides procedures to calculate statistics for Oxford Nanopore sequencing data and alignments.

This package provides software for phylogenomic inference.