Jeffrey Townsend, PhD

Welcome to cancereffectsizeR! This R package provides a variety of tools for analyzing somatic variant data and characterizing the evolutionary trajectories of cancers.

Faculty: Jeffrey Townsend, PhD

Download: GitHub / cancereffectsizeR package

Platform: R

Reference: doi.org (cancereffectsizeR)

P0PCorNS (Perturbation to 0 to Predict Correlated Network Stability) performs informative gene knockouts (One gene was in silico knocked out each time ), and uses BNW (Ziebarth et al. Bioinformatics, 2013.) to generate the Bayesian Networks, then calculates the Jensen-Shannon divergence (JSD) between networks. Finally, P0PCorNS can provide a order list of gene impacts. A gene that exhibits a higher informative impact would play an more importent role in in the gene regulatory networks (potentially function more upstream in a linear regulatory order or be the hub gene) , and will be ranked higher for gene manipulation verification experiments.

Faculty: Jeffrey Townsend, PhD; Meng Liu, PhD; Zheng Wang, PhD

Download: GitHub / P0PCorNS package

Platform: R

Reference: doi.org (P0PCorNS)

Maps the output of massprf into a file that can be used in Chimera to color proteins execute source("batchMASSPRF_To_Chimera.R") from R, which creates the batchMASSPRF_Chimera command in your local environment.

Faculty: Jeffrey Townsend, PhD

Download: GitHub / massprf-protein-coloring package

Platform: R

Jot builds upon the API of Jane (Journal/Author Name Estimator, https://jane.biosemantics.org/) to identify PubMed articles that are similar in content to a manuscript's title and abstract. Jot gathers these articles and their similarity scores together with manuscript citations and a journal metadata assembled from the National Library of Medicine (NLM) Catalog, the Directory of Open Access Journals (DOAJ), Sherpa Romeo, and impact metric databases. The result is a personalized, multi-dimensional data set that can be navigated through a series of linked, interactive plots and tables, allowing an author to sort and study journals according to the attributes most important to them.

Faculty: Jeffrey Townsend, PhD

Download: GitHub / Jot: Journal Targeter package

Platform: Python

Reference: doi.org (Jot: Journal Targeter)

MASS-PRF (Model Averaged Site Selection with Poisson Random Field theory): A program that quantifies heterogeneity of selection intensity across sites within coding sequences by using polymorphism and divergence data.

Faculty: Jeffrey Townsend, PhD; Michael Cappello, MD

Download: GitHub / MASS-PRF package

Platform: C++

Reference: doi.org (MASS-PRF)

The PhyDesign web application consists of 3 components:

1) A form to upload information and choose an application to calculate the evolutionary rates for each alignment site,

2) A table listing the site rates produced by the analysis, including links for download, and

3) A user-friendly graphical interface to plot the phylogenetic profiles and calculate integration values. This latter component produces profiles of phylogenetic informativeness, calculates net and relative (per site) informativeness over specified time intervals, and offers the ability to integrate informativeness over epochs of interest.

Faculty: Jeffrey Townsend, PhD

Download: PhyDesign package

Platform: Web app

Reference: doi.org (PhyDesign)

Implementation of LOX in R. LOX uses Markov Chain Monte Carlo to estimate Levels Of gene eXpression from high-throughput expressed sequence data sets with multiple treatments or samples. LOXR can be used to run LOX from the R console, as well as to parse and plot LOX's output.

Faculty: Jeffrey Townsend, PhD

Download: LOX package

Platform: R

MACML is a program that clusters sequences into heterogeneous regions with specific site types, without requiring any prior knowledge, such as cluster count or length, etc. It features maximum likelihood estimation, model selection and model averaging and adopts a divide-and-conquer approach to hierarchically detect clusters within sequences.

Faculty: Jeffrey Townsend, PhD

Download: MACML package

Platform: R

Reference: doi.org (MACML)

Bayesian Analysis of Gene Expression Levels (BAGEL) is a program that allows statistical inferences to be made regarding differential gene expression between two or more samples measured on spotted (two-channel) microarrays. BAGEL makes these inferences from normalized ratio data, on a gene-by-gene basis. The advantages of BAGEL include ease of use, straightforward interpretation of results, statistical robustness, flexibility in accepting different experimental designs, and that it is free. BAGEL was written by Jeffrey Townsend, who periodically updates and improves the program, and to whom bugs should be reported. BAGEL is available for Windows, Mac OS9, Mac OSX, and Linux. BAGEL can be downloaded from the Townsend Lab web site, http://www.yale.edu/townsend/software.html.

Faculty: Jeffrey Townsend, PhD

Download: BAGEL package

Platform: Unix

Reference: doi.org (BAGEL)

KaKs_Calculator adopts model selection and model averaging to calculate nonsynonymous (Ka) and synonymous (Ks) substitution rates, attempting to include as many features as needed for accurately capturing evolutionary information in protein-coding sequences. In addition, several existing methods for calculating Ka and Ks are also incorporated into KaKs_Calculator.

Faculty: Jeffrey Townsend, PhD

Download: Google Code / KaKs_Calculator package

Reference: doi.org (KaKs_Calculator)

SeqPop: A program for computing population genetic statistics on sequence data, including Pn, Theta, Pi(i,j), Kst(*), Fst(*), and their Monte Carlo significance for population subdivision.

Faculty: Jeffrey Townsend, PhD

Download: SeqPop package

Platform: Unix

Enables rapid calculation of phylogenetic information content using the latest advances in phylogenetic informativeness based theory. These advances include modifications that incorporate uneven branch lengths and any model of nucleotide substitution to provide assessments of the phylogenetic utility of any given dataset or dataset partition. Also provides new tools for data visualization and routines optimized for rapid statistical calculations, including approaches making use of Bayesian posterior distributions and parallel processing. Users can apply these approaches toward screening datasets for phylogenetic/genomic information content.

Faculty: Jeffrey Townsend, PhD

Download: CranR / PhyInformR package

Platform: R

Reference: doi.org (PhyInformR)

PathScore quantifies the level of enrichment of somatic mutations within curated pathways, applying a novel approach that identifies pathways enriched across patients. The application provides several user-friendly, interactive graphic interfaces for data exploration, including tools for comparing pathway effect sizes, significance, gene-set overlap and enrichment differences between projects.

Faculty: Jeffrey Townsend, PhD

Download: GitHub / Pathscore package

Platform: Web app

Reference: doi.org (Pathscore)