vanhemertjohn / packages

Package Name Access Summary Updated
libsbol public Synthetic Biology Open Language 2020-06-12
igv-jupyter public Jupyter extension for embedding the genome visualation igv.js in a notebook 2019-09-19
antismash public The antibiotics and Secondary Metabolites Analysis Shell. 2019-09-17
minimock public The simplest possible mock library 2019-09-17
dnaplotlib public 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. 2019-08-14
r-rehh public 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. 2019-07-25 public Contains example data for the 'rehh' package. 2019-07-25
cobra public COBRApy is a package for constraints-based modeling of biological networks 2019-06-26
depinfo public Summary of the package 2019-06-26
pipdeptree public Command line utility to show dependency tree of packages 2019-06-26
poppy public No Summary 2019-01-18
equilibrator-api public Standard reaction Gibbs energy estimation for biochemical reactions. 2019-01-18
sbtab public SBtab - Standardised Data Tables for Systems Biology 2019-01-07
rnaseq public No Summary 2018-07-06
deseq2 public 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. 2018-07-06
couchdb public Python library for working with CouchDB 2018-07-06
facs public FACS bloom filter implementation 2018-07-03
jupyterr public No Summary 2018-07-03
chipseq public No Summary 2018-06-05
r-idr public 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 2018-06-05
macs2 public Model Based Analysis for ChIP-Seq data 2018-06-05
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