Showing 35 of total 35 results (show query)
slequime
nosoi:A Forward Agent-Based Transmission Chain Simulator
The aim of 'nosoi' (pronounced no.si) is to provide a flexible agent-based stochastic transmission chain/epidemic simulator (Lequime et al. Methods in Ecology and Evolution 11:1002-1007). It is named after the daimones of plague, sickness and disease that escaped Pandora's jar in the Greek mythology. 'nosoi' is able to take into account the influence of multiple variable on the transmission process (e.g. dual-host systems (such as arboviruses), within-host viral dynamics, transportation, population structure), alone or taken together, to create complex but relatively intuitive epidemiological simulations.
Maintained by Sebastian Lequime. Last updated 2 months ago.
19.6 match 8 stars 7.26 score 30 scripts
mechantrouquin
landsepi:Landscape Epidemiology and Evolution
A stochastic, spatially-explicit, demo-genetic model simulating the spread and evolution of a plant pathogen in a heterogeneous landscape to assess resistance deployment strategies. It is based on a spatial geometry for describing the landscape and allocation of different cultivars, a dispersal kernel for the dissemination of the pathogen, and a SEIR ('Susceptible-Exposed-Infectious-Removed’) structure with a discrete time step. It provides a useful tool to assess the performance of a wide range of deployment options with respect to their epidemiological, evolutionary and economic outcomes. Loup Rimbaud, Julien Papaïx, Jean-François Rey, Luke G Barrett, Peter H Thrall (2018) <doi:10.1371/journal.pcbi.1006067>.
Maintained by Jean-François Rey. Last updated 6 months ago.
32.9 match 3.58 score 18 scripts
viralemergence
insectDisease:Ecological Database of the World's Insect Pathogens
David Onstad provided us with this insect disease database, sometimes referred to as the 'Ecological Database of the Worlds Insect Pathogens' or EDWIP. Files have been converted from 'SQL' to csv, and ported into 'R' for easy exploration and analysis. Thanks to the Macroecology of Infectious Disease Research Coordination Network (RCN) for funding and support. Data are also served online in a static format at <https://edwip.ecology.uga.edu/>.
Maintained by Tad Dallas. Last updated 2 months ago.
24.3 match 13 stars 4.41 score 2 scripts
zhenkewu
baker:"Nested Partially Latent Class Models"
Provides functions to specify, fit and visualize nested partially-latent class models ( Wu, Deloria-Knoll, Hammitt, and Zeger (2016) <doi:10.1111/rssc.12101>; Wu, Deloria-Knoll, and Zeger (2017) <doi:10.1093/biostatistics/kxw037>; Wu and Chen (2021) <doi:10.1002/sim.8804>) for inference of population disease etiology and individual diagnosis. In the motivating Pneumonia Etiology Research for Child Health (PERCH) study, because both quantities of interest sum to one hundred percent, the PERCH scientists frequently refer to them as population etiology pie and individual etiology pie, hence the name of the package.
Maintained by Zhenke Wu. Last updated 11 months ago.
bayesiancase-controllatent-class-analysisjagscpp
13.4 match 8 stars 6.00 score 21 scripts
grunwaldlab
poppr:Genetic Analysis of Populations with Mixed Reproduction
Population genetic analyses for hierarchical analysis of partially clonal populations built upon the architecture of the 'adegenet' package. Originally described in Kamvar, Tabima, and Grünwald (2014) <doi:10.7717/peerj.281> with version 2.0 described in Kamvar, Brooks, and Grünwald (2015) <doi:10.3389/fgene.2015.00208>.
Maintained by Zhian N. Kamvar. Last updated 10 months ago.
clonalitygenetic-analysisgenetic-distancesminimum-spanning-networksmultilocus-genotypesmultilocus-lineagespopulation-geneticspopulationsopenmp
6.9 match 69 stars 10.84 score 672 scripts
mrc-ide
epireview:Tools to update and summarise the latest pathogen data from the Pathogen Epidemiology Review Group (PERG)
Contains the latest open access pathogen data from the Pathogen Epidemiology Review Group (PERG). Tools are available to update pathogen databases with new peer-reviewed data as it becomes available, and to summarise the latest data using tables and figures.
Maintained by Sangeeta Bhatia. Last updated 3 days ago.
10.8 match 30 stars 6.76 score 6 scripts
bioc
HPiP:Host-Pathogen Interaction Prediction
HPiP (Host-Pathogen Interaction Prediction) uses an ensemble learning algorithm for prediction of host-pathogen protein-protein interactions (HP-PPIs) using structural and physicochemical descriptors computed from amino acid-composition of host and pathogen proteins.The proposed package can effectively address data shortages and data unavailability for HP-PPI network reconstructions. Moreover, establishing computational frameworks in that regard will reveal mechanistic insights into infectious diseases and suggest potential HP-PPI targets, thus narrowing down the range of possible candidates for subsequent wet-lab experimental validations.
Maintained by Matineh Rahmatbakhsh. Last updated 5 months ago.
proteomicssystemsbiologynetworkinferencestructuralpredictiongenepredictionnetwork
14.7 match 3 stars 4.95 score 6 scripts
openplantpathology
hagis:Analysis of Plant Pathogen Pathotype Complexities, Distributions and Diversity
Analysis of plant pathogen pathotype survey data. Functions provided calculate distribution of susceptibilities, distribution of complexities with statistics, pathotype frequency distribution, as well as diversity indices for pathotypes. This package is meant to be a direct replacement for Herrmann, Löwer and Schachtel's (1999) <doi:10.1046/j.1365-3059.1999.00325.x> Habgood-Gilmour Spreadsheet, 'HaGiS', previously used for pathotype analysis.
Maintained by Adam H. Sparks. Last updated 11 days ago.
plant-pathologypathotypepathogen-surveyvirulence analysisdifferential setassessment scalepathotype-complexitiesplant-diseasepopulation-diversities
13.6 match 1 stars 5.26 score 8 scripts
mattmar
dynamAedes:A Unified Mechanistic Model for the Population Dynamics of Invasive Aedes Mosquitoes
Generalised model for population dynamics of invasive Aedes mosquitoes. Rationale and model structure are described here: Da Re et al. (2021) <doi:10.1016/j.ecoinf.2020.101180> and Da Re et al. (2022) <doi:10.1101/2021.12.21.473628>.
Maintained by Matteo Marcantonio. Last updated 1 years ago.
ecologyinvasive-speciesmodellingmosquitoespathogens
10.0 match 7 stars 5.59 score 11 scripts
slwu89
MicroMoB:Discrete Time Simulation of Mosquito-Borne Pathogen Transmission
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 over a discrete time step.
Maintained by Sean L. Wu. Last updated 2 years ago.
13.4 match 4.16 score 32 scripts
hopkinsidd
phylosamp:Sample Size Calculations for Molecular and Phylogenetic Studies
Implements novel tools for estimating sample sizes needed for phylogenetic studies, including studies focused on estimating the probability of true pathogen transmission between two cases given phylogenetic linkage and studies focused on tracking pathogen variants at a population level. Methods described in Wohl, Giles, and Lessler (2021) and in Wohl, Lee, DiPrete, and Lessler (2023).
Maintained by Justin Lessler. Last updated 2 years ago.
6.7 match 12 stars 6.65 score 25 scriptsbioc
artMS:Analytical R tools for Mass Spectrometry
artMS provides a set of tools for the analysis of proteomics label-free datasets. It takes as input the MaxQuant search result output (evidence.txt file) and performs quality control, relative quantification using MSstats, downstream analysis and integration. artMS also provides a set of functions to re-format and make it compatible with other analytical tools, including, SAINTq, SAINTexpress, Phosfate, and PHOTON. Check [http://artms.org](http://artms.org) for details.
Maintained by David Jimenez-Morales. Last updated 5 months ago.
proteomicsdifferentialexpressionbiomedicalinformaticssystemsbiologymassspectrometryannotationqualitycontrolgenesetenrichmentclusteringnormalizationimmunooncologymultiplecomparisonanalysisanalyticalap-msbioconductorbioinformaticsmass-spectrometryphosphoproteomicspost-translational-modificationquantitative-analysis
6.5 match 14 stars 6.41 score 13 scripts
tbep-tech
peptools:Analysis Tools for Importing, Wrangling, and Summarizing Suffolk County Water Quality Data
Analysis tools for importing, wrangling, and summarizing Suffolk County water quality data. Functions are used to create reporting materials.
Maintained by Marcus Beck. Last updated 1 years ago.
9.0 match 4.33 score 54 scripts
daniel-jg
BeviMed:Bayesian Evaluation of Variant Involvement in Mendelian Disease
A fast integrative genetic association test for rare diseases based on a model for disease status given allele counts at rare variant sites. Probability of association, mode of inheritance and probability of pathogenicity for individual variants are all inferred in a Bayesian framework - 'A Fast Association Test for Identifying Pathogenic Variants Involved in Rare Diseases', Greene et al 2017 <doi:10.1016/j.ajhg.2017.05.015>.
Maintained by Daniel Greene. Last updated 10 months ago.
9.6 match 1 stars 3.41 score 17 scriptsmrc-ide
EpiEstim:Estimate Time Varying Reproduction Numbers from Epidemic Curves
Tools to quantify transmissibility throughout an epidemic from the analysis of time series of incidence as described in Cori et al. (2013) <doi:10.1093/aje/kwt133> and Wallinga and Teunis (2004) <doi:10.1093/aje/kwh255>.
Maintained by Anne Cori. Last updated 7 months ago.
2.5 match 95 stars 12.00 score 1.0k scripts 7 dependentsbioc
AlphaMissenseR:Accessing AlphaMissense Data Resources in R
The AlphaMissense publication <https://www.science.org/doi/epdf/10.1126/science.adg7492> outlines how a variant of AlphaFold / DeepMind was used to predict missense variant pathogenicity. Supporting data on Zenodo <https://zenodo.org/record/10813168> include, for instance, 71M variants across hg19 and hg38 genome builds. The 'AlphaMissenseR' package allows ready access to the data, downloading individual files to DuckDB databases for exploration and integration into *R* and *Bioconductor* workflows.
Maintained by Martin Morgan. Last updated 5 months ago.
snpannotationfunctionalgenomicsstructuralpredictiontranscriptomicsvariantannotationgenepredictionimmunooncology
3.8 match 8 stars 6.86 score 10 scripts
agrocares
OBIC:Calculate the Open Bodem Index (OBI) Score
The Open Bodem Index (OBI) is a method to evaluate the quality of soils of agricultural fields in The Netherlands and the sustainability of the current agricultural practices. The OBI score is based on four main criteria: chemical, physical, biological and management, which consist of more than 21 indicators. By providing results of a soil analysis and management info the 'OBIC' package can be use to calculate he scores, indicators and derivatives that are used by the OBI. More information about the Open Bodem Index can be found at <https://openbodemindex.nl/>.
Maintained by Sven Verweij. Last updated 6 months ago.
3.4 match 11 stars 6.82 score 20 scripts
rjknell
Biostatistics:Statistics Tutorials for Biologists
Tutorials for statistics, aimed at biological scientists. Subjects range from basic descriptive statistics through to complex linear modelling. The tutorials include text, videos, interactive coding exercises and multiple choice quizzes. The package also includes 19 datasets which are used in the tutorials.
Maintained by Rob Knell. Last updated 3 years ago.
3.6 match 4.54 score 5 scripts
daijiang
neonDivData:Standardized NEON Organismal Data for Biodiversity Research
Cleaned, simplified, and standardized NEON organismal data for biodiversity research. The following taxonomic groups are included so far: algae, beetles, birds, fish, herptiles, macroinvertebrates, mosquitoes, plants, small_mammals, ticks, tick_pathogens, and zooplankton. NEON input data (<https://data.neonscience.org>) were processed and standardized using R package `ecocomDP` (<https://github.com/EDIorg/ecocomDP>).
Maintained by Daijiang Li. Last updated 10 months ago.
3.8 match 15 stars 4.18 score 17 scripts
ahgroup
DSAIDE:Dynamical Systems Approach to Infectious Disease Epidemiology (Ecology/Evolution)
Exploration of simulation models (apps) of various infectious disease transmission dynamics scenarios. The purpose of the package is to help individuals learn about infectious disease epidemiology (ecology/evolution) from a dynamical systems perspective. All apps include explanations of the underlying models and instructions on what to do with the models.
Maintained by Andreas Handel. Last updated 1 years ago.
1.7 match 26 stars 6.30 score 22 scripts
zkamvar
repvar:Extract Samples to Represent All Variables
In population genetics, it's not uncommon to re-genotype sets of samples to use as positive controls in future studies or for diagnostic panels. To save cost, it's often desireable to have the minimum number of samples that represent all of the alleles in the data. This package provides a procedure that will select these samples with alternative options. The name 'repvar' stands for 'REPresent VARiables'.
Maintained by Zhian N. Kamvar. Last updated 2 months ago.
3.5 match 2.70 score 1 scripts
ocbe-uio
contingencytables:Statistical Analysis of Contingency Tables
Provides functions to perform statistical inference of data organized in contingency tables. This package is a companion to the "Statistical Analysis of Contingency Tables" book by Fagerland et al. <ISBN 9781466588172>.
Maintained by Waldir Leoncio. Last updated 7 months ago.
2.0 match 3 stars 4.13 score 8 scripts 1 dependents
cran
StrainRanking:Ranking of Pathogen Strains
Regression-based ranking of pathogen strains with respect to their contributions to natural epidemics, using demographic and genetic data sampled in the curse of the epidemics. This package also includes the GMCPIC test.
Maintained by Samuel Soubeyrand. Last updated 7 years ago.
7.7 match 1.00 score
mdhall272
STraTUS:Enumeration and Uniform Sampling of Transmission Trees for a Known Phylogeny
For a single, known pathogen phylogeny, provides functions for enumeration of the set of compatible epidemic transmission trees, and for uniform sampling from that set. Optional arguments allow for incomplete sampling with a known number of missing individuals, multiple sampling, and known infection time limits. Always assumed are a complete transmission bottleneck and no superinfection or reinfection. See Hall and Colijn (2019) <doi:10.1093/molbev/msz058> for methodology.
Maintained by Matthew Hall. Last updated 5 months ago.
2.2 match 4 stars 3.30 scoremechantrouquin
SMITIDvisu:Visualize Data for Host and Viral Population from 'SMITIDstruct' using 'HTMLwidgets'
Visualisation tools for 'SMITIDstruct' package. Allow to visualize host timeline, transmission tree, index diversities and variant graph using 'HTMLwidgets'. It mainly using 'D3JS' javascript framework.
Maintained by Jean-Francois Rey. Last updated 4 years ago.
4.0 match 1.63 score 43 scripts
acorg
Racmacs:Antigenic Cartography Macros
A toolkit for making antigenic maps from immunological assay data, in order to quantify and visualize antigenic differences between different pathogen strains as described in Smith et al. (2004) <doi:10.1126/science.1097211> and used in the World Health Organization influenza vaccine strain selection process. Additional functions allow for the diagnostic evaluation of antigenic maps and an interactive viewer is provided to explore antigenic relationships amongst several strains and incorporate the visualization of associated genetic information.
Maintained by Sam Wilks. Last updated 9 months ago.
0.5 match 21 stars 8.06 score 362 scriptsbioc
rhinotypeR:Rhinovirus genotyping
"rhinotypeR" is designed to automate the comparison of sequence data against prototype strains, streamlining the genotype assignment process. By implementing predefined pairwise distance thresholds, this package makes genotype assignment accessible to researchers and public health professionals. This tool enhances our epidemiological toolkit by enabling more efficient surveillance and analysis of rhinoviruses (RVs) and other viral pathogens with complex genomic landscapes. Additionally, "rhinotypeR" supports comprehensive visualization and analysis of single nucleotide polymorphisms (SNPs) and amino acid substitutions, facilitating in-depth genetic and evolutionary studies.
Maintained by Martha Luka. Last updated 5 months ago.
sequencinggeneticsphylogenetics
0.5 match 4 stars 6.28 score 2 scripts
knausb
pinfsc50:Sequence ('FASTA'), Annotation ('GFF') and Variants ('VCF') for 17 Samples of 'P. Infestans" and 1 'P. Mirabilis'
Genomic data for the plant pathogen "Phytophthora infestans." It includes a variant file ('VCF'), a sequence file ('FASTA') and an annotation file ('GFF'). This package is intended to be used as example data for packages that work with genomic data.
Maintained by Brian J. Knaus. Last updated 1 years ago.
0.5 match 5.62 score 34 scripts 20 dependentsbioc
mobileRNA:mobileRNA: Investigate the RNA mobilome & population-scale changes
Genomic analysis can be utilised to identify differences between RNA populations in two conditions, both in production and abundance. This includes the identification of RNAs produced by multiple genomes within a biological system. For example, RNA produced by pathogens within a host or mobile RNAs in plant graft systems. The mobileRNA package provides methods to pre-process, analyse and visualise the sRNA and mRNA populations based on the premise of mapping reads to all genotypes at the same time.
Maintained by Katie Jeynes-Cupper. Last updated 5 months ago.
visualizationrnaseqsequencingsmallrnagenomeassemblyclusteringexperimentaldesignqualitycontrolworkflowstepalignmentpreprocessingbioinformaticsplant-science
0.5 match 4 stars 5.00 score 2 scripts
sarahleavitt
nbTransmission:Naive Bayes Transmission Analysis
Estimates the relative transmission probabilities between cases in an infectious disease outbreak or cluster using naive Bayes. Included are various functions to use these probabilities to estimate transmission parameters such as the generation/serial interval and reproductive number as well as finding the contribution of covariates to the probabilities and visualizing results. The ideal use is for an infectious disease dataset with metadata on the majority of cases but more informative data such as contact tracing or pathogen whole genome sequencing on only a subset of cases. For a detailed description of the methods see Leavitt et al. (2020) <doi:10.1093/ije/dyaa031>.
Maintained by Sarah V Leavitt. Last updated 5 days ago.
0.5 match 4 stars 4.45 score 14 scriptsbioc
pmm:Parallel Mixed Model
The Parallel Mixed Model (PMM) approach is suitable for hit selection and cross-comparison of RNAi screens generated in experiments that are performed in parallel under several conditions. For example, we could think of the measurements or readouts from cells under RNAi knock-down, which are infected with several pathogens or which are grown from different cell lines.
Maintained by Anna Drewek. Last updated 5 months ago.
0.5 match 4.15 score 3 scripts
philipagnew
anovir:Analysis of Virulence
Epidemiological population dynamics models traditionally define a pathogen's virulence as the increase in the per capita rate of mortality of infected hosts due to infection. This package provides functions allowing virulence to be estimated by maximum likelihood techniques. The approach is based on the analysis of relative survival comparing survival in matching cohorts of infected vs. uninfected hosts (Agnew 2019) <doi:10.1101/530709>.
Maintained by Philip Agnew. Last updated 4 years ago.
0.5 match 3.34 score 20 scriptsbioc
DeProViR:A Deep-Learning Framework Based on Pre-trained Sequence Embeddings for Predicting Host-Viral Protein-Protein Interactions
Emerging infectious diseases, exemplified by the zoonotic COVID-19 pandemic caused by SARS-CoV-2, are grave global threats. Understanding protein-protein interactions (PPIs) between host and viral proteins is essential for therapeutic targets and insights into pathogen replication and immune evasion. While experimental methods like yeast two-hybrid screening and mass spectrometry provide valuable insights, they are hindered by experimental noise and costs, yielding incomplete interaction maps. Computational models, notably DeProViR, predict PPIs from amino acid sequences, incorporating semantic information with GloVe embeddings. DeProViR employs a Siamese neural network, integrating convolutional and Bi-LSTM networks to enhance accuracy. It overcomes the limitations of feature engineering, offering an efficient means to predict host-virus interactions, which holds promise for antiviral therapies and advancing our understanding of infectious diseases.
Maintained by Matineh Rahmatbakhsh. Last updated 5 months ago.
proteomicssystemsbiologynetworkinferenceneuralnetworknetwork
0.5 match 1 stars 3.00 score 1 scripts
jferdy
fluoSurv:Estimate Insect Survival from Fluorescence Data
Use spectrophotometry measurements performed on insects as a way to infer pathogens virulence. Insect movements cause fluctuations in fluorescence signal, and functions are provided to estimate when the insect has died as the moment when variance in autofluorescence signal drops to zero. The package provides functions to obtain this estimate together with functions to import spectrophotometry data from a Biotek microplate reader. Details of the method are given in Parthuisot et al. (2018) <doi:10.1101/297929>.
Maintained by Jean-Baptiste Ferdy. Last updated 7 years ago.
0.5 match 1.00 score 3 scripts