Showing 40 of total 40 results (show query)
nakarinp
longreadvqs:Viral Quasispecies Comparison from Long-Read Sequencing Data
Performs variety of viral quasispecies diversity analyses [see Pamornchainavakul et al. (2024) <doi:10.21203/rs.3.rs-4637890/v1>] based on long-read sequence alignment. Main functions include 1) sequencing error and other noise minimization and read sampling, 2) Single nucleotide variant (SNV) profiles comparison, and 3) viral quasispecies profiles comparison and visualization.
Maintained by Nakarin Pamornchainavakul. Last updated 7 months ago.
18.3 match 4.65 score 4 scripts
ahgroup
DSAIRM:Dynamical Systems Approach to Immune Response Modeling
Simulation models (apps) of various within-host immune response scenarios. The purpose of the package is to help individuals learn about within-host infection and immune response modeling 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 8 months ago.
11.8 match 34 stars 6.19 score 23 scripts
pendy05
vDiveR:Visualization of Viral Protein Sequence Diversity Dynamics
To ease the visualization of outputs from Diversity Motif Analyser ('DiMA'; <https://github.com/BVU-BILSAB/DiMA>). 'vDiveR' allows visualization of the diversity motifs (index and its variants – major, minor and unique) for elucidation of the underlying inherent dynamics. Please refer <https://vdiver-manual.readthedocs.io/en/latest/> for more information.
Maintained by Pendy Tok. Last updated 2 months ago.
conservation-leveldiversityentropysequencesviralvisualization
13.9 match 3.78 score 4 scripts
juanv66x
viraldomain:Applicability Domain Methods of Viral Load and CD4 Lymphocytes
Provides methods for assessing the applicability domain of models that predict viral load and CD4 (Cluster of Differentiation 4) lymphocyte counts. These methods help determine the extent of extrapolation when making predictions.
Maintained by Juan Pablo Acuña González. Last updated 5 months ago.
applicability-domaincd4-lymphocytesviral-load
14.3 match 3.34 score 22 scriptsjuanv66x
qvirus:Quantum Computing for Analyzing CD4 Lymphocytes and Antiretroviral Therapy
Resources, tutorials, and code snippets dedicated to exploring the intersection of quantum computing and artificial intelligence (AI) in the context of analyzing Cluster of Differentiation 4 (CD4) lymphocytes and optimizing antiretroviral therapy (ART) for human immunodeficiency virus (HIV). With the emergence of quantum artificial intelligence and the development of small-scale quantum computers, there's an unprecedented opportunity to revolutionize the understanding of HIV dynamics and treatment strategies. This project leverages the R package 'qsimulatR' (Ostmeyer and Urbach, 2023, <https://CRAN.R-project.org/package=qsimulatR>), a quantum computer simulator, to explore these applications in quantum computing techniques, addressing the challenges in studying CD4 lymphocytes and enhancing ART efficacy.
Maintained by Juan Pablo Acuña González. Last updated 12 days ago.
8.6 match 5.43 score 15 scripts
ecomets
npde:Normalised Prediction Distribution Errors for Nonlinear Mixed-Effect Models
Provides routines to compute normalised prediction distribution errors, a metric designed to evaluate non-linear mixed effect models such as those used in pharmacokinetics and pharmacodynamics.
Maintained by Emmanuelle Comets. Last updated 1 years ago.
10.5 match 3.70 score 119 scripts 7 dependents
sineadmorris
ushr:Understanding Suppression of HIV
Analyzes longitudinal data of HIV decline in patients on antiretroviral therapy using the canonical biphasic exponential decay model (pioneered, for example, by work in Perelson et al. (1997) <doi:10.1038/387188a0>; and Wu and Ding (1999) <doi:10.1111/j.0006-341X.1999.00410.x>). Model fitting and parameter estimation are performed, with additional options to calculate the time to viral suppression. Plotting and summary tools are also provided for fast assessment of model results.
Maintained by Sinead E. Morris. Last updated 5 years ago.
9.4 match 2 stars 4.04 score 11 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.
7.3 match 13 stars 4.41 score 2 scripts
sacema
inctools:Incidence Estimation Tools
Tools for estimating incidence from biomarker data in cross- sectional surveys, and for calibrating tests for recent infection. Implements and extends the method of Kassanjee et al. (2012) <doi:10.1097/EDE.0b013e3182576c07>.
Maintained by Eduard Grebe. Last updated 4 years ago.
biomarkersbiostatisticsepidemiologyhivincidenceincidence-estimationincidence-inferenceinfectious-diseasesstatistics
4.7 match 6 stars 6.51 score 27 scripts
bioc
VERSO:Viral Evolution ReconStructiOn (VERSO)
Mutations that rapidly accumulate in viral genomes during a pandemic can be used to track the evolution of the virus and, accordingly, unravel the viral infection network. To this extent, sequencing samples of the virus can be employed to estimate models from genomic epidemiology and may serve, for instance, to estimate the proportion of undetected infected people by uncovering cryptic transmissions, as well as to predict likely trends in the number of infected, hospitalized, dead and recovered people. VERSO is an algorithmic framework that processes variants profiles from viral samples to produce phylogenetic models of viral evolution. The approach solves a Boolean Matrix Factorization problem with phylogenetic constraints, by maximizing a log-likelihood function. VERSO includes two separate and subsequent steps; in this package we provide an R implementation of VERSO STEP 1.
Maintained by Davide Maspero. Last updated 2 days ago.
biomedicalinformaticssequencingsomaticmutation
4.1 match 7 stars 6.15 scorebioc
ELViS:An R Package for Estimating Copy Number Levels of Viral Genome Segments Using Base-Resolution Read Depth Profile
Base-resolution copy number analysis of viral genome. Utilizes base-resolution read depth data over viral genome to find copy number segments with two-dimensional segmentation approach. Provides publish-ready figures, including histograms of read depths, coverage line plots over viral genome annotated with copy number change events and viral genes, and heatmaps showing multiple types of data with integrative clustering of samples.
Maintained by Jin-Young Lee. Last updated 12 days ago.
copynumbervariationcoveragegenomicvariationbiomedicalinformaticssequencingnormalizationvisualizationclustering
5.3 match 4.70 score 7 scriptsbioc
QSutils:Quasispecies Diversity
Set of utility functions for viral quasispecies analysis with NGS data. Most functions are equally useful for metagenomic studies. There are three main types: (1) data manipulation and exploration—functions useful for converting reads to haplotypes and frequencies, repairing reads, intersecting strand haplotypes, and visualizing haplotype alignments. (2) diversity indices—functions to compute diversity and entropy, in which incidence, abundance, and functional indices are considered. (3) data simulation—functions useful for generating random viral quasispecies data.
Maintained by Mercedes Guerrero-Murillo. Last updated 5 months ago.
softwaregeneticsdnaseqgeneticvariabilitysequencingalignmentsequencematchingdataimport
4.1 match 5.56 score 8 scripts 1 dependents
wilkelab
sicegar:Analysis of Single-Cell Viral Growth Curves
Aims to quantify time intensity data by using sigmoidal and double sigmoidal curves. It fits straight lines, sigmoidal, and double sigmoidal curves on to time vs intensity data. Then all the fits are used to make decision on which model best describes the data. This method was first developed in the context of single-cell viral growth analysis (for details, see Caglar et al. (2018) <doi:10.7717/peerj.4251>), and the package name stands for "SIngle CEll Growth Analysis in R".
Maintained by Claus O. Wilke. Last updated 4 years ago.
3.4 match 9 stars 6.57 score 41 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
4.0 match 3 stars 4.95 score 6 scripts
metrumresearchgroup
mrgsolve:Simulate from ODE-Based Models
Fast simulation from ordinary differential equation (ODE) based models typically employed in quantitative pharmacology and systems biology.
Maintained by Kyle T Baron. Last updated 1 months ago.
1.8 match 138 stars 10.90 score 1.2k scripts 3 dependents
sergejruff
Virusparies:Visualize and Process Output from 'VirusHunterGatherer'
A collection of tools for downstream analysis of 'VirusHunterGatherer' output. Processing of hittables and plotting of results, enabling better interpretation, is made easier with the provided functions.
Maintained by Ruff Sergej. Last updated 3 months ago.
bioinformaticsdata-drivendiscoverdiscoveryggplot2graphical-tablehidden-markov-modelhmmlearnplotr-programmingsummary-statisticsvirusvirus-discoveryvirus-scanningvirusgatherervirushuntervirushuntergatherervisualization
4.3 match 1 stars 4.49 score 28 scripts
greshamlab
vivaldi:Viral Variant Location and Diversity
Analysis of minor alleles in Illumina sequencing data of viral genomes. Functions in 'vivaldi' primarily operate on vcf files.
Maintained by David Gresham. Last updated 1 years ago.
3.7 match 3 stars 4.78 score 7 scripts
ai4ci
ggoutbreak:Estimate Incidence, Proportions and Exponential Growth Rates
Simple statistical models and visualisations for calculating the incidence, proportion, exponential growth rate, and reproduction number of infectious disease case time series. This toolkit was largely developed during the COVID-19 pandemic.
Maintained by Robert Challen. Last updated 1 months ago.
3.6 match 1 stars 4.30 scorebioc
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
4.9 match 1 stars 3.00 score 1 scripts
johnjsl7
daewr:Design and Analysis of Experiments with R
Contains Data frames and functions used in the book "Design and Analysis of Experiments with R", Lawson(2015) ISBN-13:978-1-4398-6813-3.
Maintained by John Lawson. Last updated 2 years ago.
3.4 match 3 stars 3.83 score 217 scripts 3 dependents
usaid-mozambique
sismar:Arrumar dados SISMA
Fornece um conjunto de funções para a criação de conjuntos de dados analíticos a partir de downloads do SISMA e DISA. Inclui funções que arrumam os ficheiros para um formato longo, removem variáveis desnecessárias, e criam colunas úteis para a análise.
Maintained by Joe Lara. Last updated 12 days ago.
1.7 match 2 stars 5.24 score 9 scripts
crtahlin
peRiodiCS:Functions for Generating Periodic Curves
Functions for generating variants of curves: restricted cubic spline, periodic restricted cubic spline, periodic cubic spline. Periodic splines can be used to model data that has periodic nature / seasonality.
Maintained by Crt Ahlin. Last updated 7 years ago.
3.2 match 1 stars 2.70 score 2 scripts
darwin-eu
TreatmentPatterns:Analyzes Real-World Treatment Patterns of a Study Population of Interest
Computes treatment patterns within a given cohort using the Observational Medical Outcomes Partnership (OMOP) common data model (CDM). As described in Markus, Verhamme, Kors, and Rijnbeek (2022) <doi:10.1016/j.cmpb.2022.107081>.
Maintained by Maarten van Kessel. Last updated 6 days ago.
1.3 match 2 stars 6.62 score 65 scriptsbioc
HoloFoodR:R interface to EBI HoloFood resource
Utility package to facilitate integration and analysis of EBI HoloFood data in R. This package streamlines access to the resource, allowing for direct loading of data into formats optimized for downstream analytics.
Maintained by Tuomas Borman. Last updated 5 months ago.
softwareinfrastructuredataimport
1.7 match 1 stars 4.74 score 6 scripts
mechantrouquin
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.
4.5 match 1.63 score 43 scripts
kristyrobledo
VarReg:Semi-Parametric Variance Regression
Methods for fitting semi-parametric mean and variance models, with normal or censored data. Extended to allow a regression in the location, scale and shape parameters, and further for multiple regression in each.
Maintained by Kristy Robledo. Last updated 2 years ago.
1.2 match 1 stars 4.46 score 29 scripts
cran
SMITIDstruct:Data Structure and Manipulations Tool for Host and Viral Population
Statistical Methods for Inferring Transmissions of Infectious Diseases from deep sequencing data (SMITID). It allow sequence-space-time host and viral population data storage, indexation and querying.
Maintained by Jean-Francois Rey. Last updated 6 years ago.
5.1 match 1.00 score
chedgala
qrNLMM:Quantile Regression for Nonlinear Mixed-Effects Models
Quantile regression (QR) for Nonlinear Mixed-Effects Models via the asymmetric Laplace distribution (ALD). It uses the Stochastic Approximation of the EM (SAEM) algorithm for deriving exact maximum likelihood estimates and full inference results for the fixed-effects and variance components. It also provides prediction and graphical summaries for assessing the algorithm convergence and fitting results.
Maintained by Christian E. Galarza. Last updated 8 months ago.
3.8 match 2 stars 1.30 score 5 scripts
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.
0.5 match 8 stars 7.26 score 30 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 scriptsbioc
ISAnalytics:Analyze gene therapy vector insertion sites data identified from genomics next generation sequencing reads for clonal tracking studies
In gene therapy, stem cells are modified using viral vectors to deliver the therapeutic transgene and replace functional properties since the genetic modification is stable and inherited in all cell progeny. The retrieval and mapping of the sequences flanking the virus-host DNA junctions allows the identification of insertion sites (IS), essential for monitoring the evolution of genetically modified cells in vivo. A comprehensive toolkit for the analysis of IS is required to foster clonal trackign studies and supporting the assessment of safety and long term efficacy in vivo. This package is aimed at (1) supporting automation of IS workflow, (2) performing base and advance analysis for IS tracking (clonal abundance, clonal expansions and statistics for insertional mutagenesis, etc.), (3) providing basic biology insights of transduced stem cells in vivo.
Maintained by Francesco Gazzo. Last updated 3 months ago.
biomedicalinformaticssequencingsinglecell
0.5 match 3 stars 5.83 score 15 scriptsbioc
TrIdent:TrIdent - Transduction Identification
The `TrIdent` R package automates the analysis of transductomics data by detecting, classifying, and characterizing read coverage patterns associated with potential transduction events. Transductomics is a DNA sequencing-based method for the detection and characterization of transduction events in pure cultures and complex communities. Transductomics relies on mapping sequencing reads from a viral-like particle (VLP)-fraction of a sample to contigs assembled from the metagenome (whole-community) of the same sample. Reads from bacterial DNA carried by VLPs will map back to the bacterial contigs of origin creating read coverage patterns indicative of ongoing transduction.
Maintained by Jessie Maier. Last updated 14 days ago.
coveragemetagenomicspatternlogicclassificationsequencingbacteriophagehorizontal-gene-transferpattern-matchingphagesequencing-coveragetransductiontransductomicsvirus-like-particle
0.5 match 2 stars 5.04 score 7 scripts
ludwighoon
minSNPs:Resolution-Optimised SNPs Searcher
This is a R implementation of "Minimum SNPs" software as described in "Price E.P., Inman-Bamber, J., Thiruvenkataswamy, V., Huygens, F and Giffard, P.M." (2007) <doi:10.1186/1471-2105-8-278> "Computer-aided identification of polymorphism sets diagnostic for groups of bacterial and viral genetic variants."
Maintained by Ludwig Kian Soon Hoon. Last updated 12 months ago.
0.5 match 3 stars 4.76 score 38 scriptsjuanv66x
viralx:Explainers for Regression Models in HIV Research
A dedicated viral-explainer model tool designed to empower researchers in the field of HIV research, particularly in viral load and CD4 (Cluster of Differentiation 4) lymphocytes regression modeling. Drawing inspiration from the 'tidymodels' framework for rigorous model building of Max Kuhn and Hadley Wickham (2020) <https://www.tidymodels.org>, and the 'DALEXtra' tool for explainability by Przemyslaw Biecek (2020) <doi:10.48550/arXiv.2009.13248>. It aims to facilitate interpretable and reproducible research in biostatistics and computational biology for the benefit of understanding HIV dynamics.
Maintained by Juan Pablo Acuña González. Last updated 4 months ago.
0.8 match 3.00 score 1 scripts
molevolepid
SEEPS:Sequence evolution and epidemiological process simulator
A modular, modern simulation suite and toolkit for simulating transmission networks, phylogenies, and evolutionary pairwise distance matrices under different models and assumptions for viral/sequence evolution. While intially developed for HIV, SEEPS offers modular utilities for custom workflows for extension beyond HIV.
Maintained by Michael Kupperman. Last updated 2 months ago.
biological-sequencesepidemiologyevolutionhivsimulation-framework
0.5 match 1 stars 3.95 score 6 scripts
lbbe-software
Mondrian:A Simple Graphical Representation of the Relative Occurrence and Co-Occurrence of Events
The unique function of this package allows representing in a single graph the relative occurrence and co-occurrence of events measured in a sample. As examples, the package was applied to describe the occurrence and co-occurrence of different species of bacterial or viral symbionts infecting arthropods at the individual level. The graphics allows determining the prevalence of each symbiont and the patterns of multiple infections (i.e. how different symbionts share or not the same individual hosts). We named the package after the famous painter as the graphical output recalls Mondrian’s paintings.
Maintained by Aurélie Siberchicot. Last updated 8 months ago.
0.5 match 2 stars 4.00 score 8 scriptscran
SeqFeatR:A Tool to Associate FASTA Sequences and Features
Provides user friendly methods for the identification of sequence patterns that are statistically significantly associated with a property of the sequence. For instance, SeqFeatR allows to identify viral immune escape mutations for hosts of given HLA types. The underlying statistical method is Fisher's exact test, with appropriate corrections for multiple testing, or Bayes. Patterns may be point mutations or n-tuple of mutations. SeqFeatR offers several ways to visualize the results of the statistical analyses, see Budeus (2016) <doi:10.1371/journal.pone.0146409>.
Maintained by Bettina Budeus. Last updated 6 years ago.
0.5 match 2.30 score
wagner-s
MultIS:Reconstruction of Clones from Integration Site Readouts and Visualization
Tools necessary to reconstruct clonal affiliations from temporally and/or spatially separated measurements of viral integration sites. For this means it utilizes correlations present in the relative readouts of the integration sites. Furthermore, facilities for filtering of the data and visualization of different steps in the pipeline are provided with the package.
Maintained by Sebastian Wagner. Last updated 4 years ago.
0.5 match 2.00 score 1 scripts