vanhemertjohn
by John Van Hemert
Formally trained in Computational Biology, Multivariate Statistics, and Machine Learning. Leads a global group of statisticians, analysts, computational biologists, and data scientists dedicated to R&D efforts.
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Packages
| Name | Latest Version | Summary | Updated | License |
|---|
| antismash | 5.0.0 | The antibiotics and Secondary Metabolites Analysis Shell. | Mar 25, 2025 | GNU Affero General Public License v3 or later (AGPLv3+) |
| chipseq | 0.0.0 | — | Mar 25, 2025 | — |
| cobra | 0.15.3 | COBRApy is a package for constraints-based modeling of biological networks | Mar 25, 2025 | GNU Lesser General Public License v2 or later (LGPLv2+) or GNU General Public v2 or later (GPLv2+) |
| couchdb | 1.2 | Python library for working with CouchDB | Mar 25, 2025 | BSD License |
| depinfo | 1.5.1 | Summary of the package | Mar 25, 2025 | Apache Software |
| deseq2 | 1.18.1 | Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. | Mar 25, 2025 | LGPL (>= 3) |
| dnaplotlib | 1.0 | DNAplotlib is a library that enables highly customizable visualization of individual genetic constructs and libraries of design variants. It can be thought of in many ways as matplotlib for genetic diagrams. Publication quality vector-based output is produced and all aspects of the rendering process can be easily customized or replaced by the user. DNAplotlib is capable of SBOL Visual compliant diagrams in addition to a format able to better illustrate the precise location and length of each genetic part. This alternative "traced-based" visualization method enables direct comparison with nucleotide-level information such as RNA-seq read depth or other base resolution measures. While it is envisaged that access will be predominantly via the programming interface, several easy to use text-based input formats can be processed by a command-line scripts to facilitate broader usage. DNAplotlib is cross-platform and open-source software released under the OSI OSL-3.0 license. | Mar 25, 2025 | MIT |
| equilibrator-api | 0.1.26 | Standard reaction Gibbs energy estimation for biochemical reactions. | Mar 25, 2025 | MIT License |
| facs | 2.0 | FACS bloom filter implementation | Mar 25, 2025 | GPLv3 |
| igv-jupyter | 0.9.7 | Jupyter extension for embedding the genome visualation igv.js in a notebook | Mar 25, 2025 | MIT |
| jupyterr | 1.0.0 | — | Mar 25, 2025 | — |
| libsbol | 2.3.0 | Synthetic Biology Open Language | Mar 25, 2025 | Apache2 |
| macs2 | 2.1.1.20160309 | Model Based Analysis for ChIP-Seq data | Mar 25, 2025 | BSD License |
| minimock | 1.2.8 | The simplest possible mock library | Mar 25, 2025 | MIT |
| pipdeptree | 0.13.2 | Command line utility to show dependency tree of packages | Mar 25, 2025 | MIT |
| poppy | 0.1.3 | — | Mar 25, 2025 | — |
| r-idr | 1.2 | This is a package for estimating the copula mixture model and plotting correspondence curves in "Measuring reproducibility of high-throughput experiments" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779, by Li, Brown, Huang, and Bickel | Mar 25, 2025 | GPL (>= 2.0) |
| r-rehh | 3.0.1 | Population genetic data such as 'Single Nucleotide Polymorphisms' (SNPs) is often used to identify genomic regions that have been under recent natural or artificial selection and might provide clues about the molecular mechanisms of adaptation. One approach, the concept of an 'Extended Haplotype Homozygosity' (EHH), introduced by (Sabeti 2002) <doi:10.1038/nature01140>, has given rise to several statistics designed for whole genome scans. The package provides functions to compute three of these, namely: 'iHS' (Voight 2006) <doi:10.1371/journal.pbio.0040072> for detecting positive or 'Darwinian' selection within a single population as well as 'Rsb' (Tang 2007) <doi:10.1371/journal.pbio.0050171> and 'XP-EHH' (Sabeti 2007) <doi:10.1038/nature06250>, targeted at differential selection between two populations. Various plotting functions are also included to facilitate visualization and interpretation of these statistics. Due to changes in the API, albeit mostly minor, this version is not compatible with versions 2.0.X. | Mar 25, 2025 | GPL (>= 2) |
| r-rehh.data | 1.0.0 | Contains example data for the 'rehh' package. | Mar 25, 2025 | GPL (>= 2) |
| rnaseq | 1.0.0 | — | Mar 25, 2025 | — |
| sbtab | 0.9.65 | SBtab - Standardised Data Tables for Systems Biology | Mar 25, 2025 | MIT |