Title: Discrete Time Simulation of Mosquito-Borne Pathogen Transmission
person("Sean L.", "Wu", email = "slwood89@gmail.com", role = c("aut","cre"), comment = c(ORCID = "0000-0002-5781-9493")),
person("David L.", "Smith", email = "smitdave@uw.edu", role = "aut", comment = c(ORCID = "0000-0003-4367-3849")),
person("Sophie", "Libkind", role = "ctb")
Description: Provides a framework based on S3 dispatch for constructing models
of mosquito-borne pathogen transmission which are constructed from submodels of various
components (i.e. immature and adult mosquitoes, human populations). A consistent mathematical
expression for the distribution of bites on hosts means that different models
(stochastic, deterministic, etc.) can be coherently incorporated and updated
Imports: extraDistr, abind, jsonlite, plumber, httpuv
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), ggplot2, data.table,

Suggests: knitr, rmarkdown, testthat (>= 3.0.0), ggplot2, data.table

Description: Measures niche breadth and overlap of microbial taxa from large matrices.
Niche breadth measurements include Levins' niche breadth (Bn) index, Hurlbert's Bn
and Feinsinger's proportional similarity (PS) index. (Feinsinger, P., Spears, E.E.,
Poole, R.W. (1981) <doi:10.2307/1936664>). Niche overlap measurements include
Levin's Overlap (Ludwig, J.A. and Reynolds, J.F. (1988, ISBN:0471832359)) and a Jaccard
similarity index of Feinsinger's PS values between taxa pairs, as Proportional Overlap.
Packaged: 2020-01-19 01:15:03 UTC; damienfinn

Title: Sequence Error Filtering Pipeline for FFPE Samples
Description: Clinical sequencing of tumor is usually performed on formalin-fixed
and paraffin-embedded (FFPE) samples and have many sequencing errors. We
found that the majority of these errors are detected in chimeric read
caused by single-strand DNA with microhomology. Our filtering pipeline
focuses on the uneven distribution of the artifacts in each read and removes
such errors in FFPE samples without over-eliminating the true mutations
Imports: tidyr, openxlsx, data.table, R.utils, stringr, magrittr,
dplyr, gtools, Biostrings, GenomicAlignments, Rsamtools,