Showing 19 of total 19 results (show query)
billdenney
PKNCA:Perform Pharmacokinetic Non-Compartmental Analysis
Compute standard Non-Compartmental Analysis (NCA) parameters for typical pharmacokinetic analyses and summarize them.
Maintained by Bill Denney. Last updated 1 months ago.
ncanoncompartmental-analysispharmacokinetics
29.4 match 73 stars 12.53 score 214 scripts 4 dependents
imamachi-n
bridger2:Genome-Wide RNA Degradation Analysis Using BRIC-Seq Data
BRIC-seq is a genome-wide approach for determining RNA stability in mammalian cells. This package provides a series of functions for performing quality check of your BRIC-seq data, calculation of RNA half-life for each transcript and comparison of RNA half-lives between two conditions.
Maintained by Naoto Imamachi. Last updated 8 years ago.
bioinformaticsbric-seqhalf-lifengsrnarpkm-values
50.1 match 3 stars 3.43 score 18 scripts
insightrx
clinPK:Clinical Pharmacokinetics Toolkit
Provides equations commonly used in clinical pharmacokinetics and clinical pharmacology, such as equations for dose individualization, compartmental pharmacokinetics, drug exposure, anthropomorphic calculations, clinical chemistry, and conversion of common clinical parameters. Where possible and relevant, it provides multiple published and peer-reviewed equations within the respective R function.
Maintained by Ron Keizer. Last updated 3 months ago.
clinical-researchpharmacokinetics
13.7 match 31 stars 6.66 score 55 scripts
bioc
rifi:'rifi' analyses data from rifampicin time series created by microarray or RNAseq
'rifi' analyses data from rifampicin time series created by microarray or RNAseq. 'rifi' is a transcriptome data analysis tool for the holistic identification of transcription and decay associated processes. The decay constants and the delay of the onset of decay is fitted for each probe/bin. Subsequently, probes/bins of equal properties are combined into segments by dynamic programming, independent of a existing genome annotation. This allows to detect transcript segments of different stability or transcriptional events within one annotated gene. In addition to the classic decay constant/half-life analysis, 'rifi' detects processing sites, transcription pausing sites, internal transcription start sites in operons, sites of partial transcription termination in operons, identifies areas of likely transcriptional interference by the collision mechanism and gives an estimate of the transcription velocity. All data are integrated to give an estimate of continous transcriptional units, i.e. operons. Comprehensive output tables and visualizations of the full genome result and the individual fits for all probes/bins are produced.
Maintained by Jens Georg. Last updated 5 months ago.
rnaseqdifferentialexpressiongeneregulationtranscriptomicsregressionmicroarraysoftware
10.1 match 4.60 score 1 scripts
jclavel
mvMORPH:Multivariate Comparative Tools for Fitting Evolutionary Models to Morphometric Data
Fits multivariate (Brownian Motion, Early Burst, ACDC, Ornstein-Uhlenbeck and Shifts) models of continuous traits evolution on trees and time series. 'mvMORPH' also proposes high-dimensional multivariate comparative tools (linear models using Generalized Least Squares and multivariate tests) based on penalized likelihood. See Clavel et al. (2015) <DOI:10.1111/2041-210X.12420>, Clavel et al. (2019) <DOI:10.1093/sysbio/syy045>, and Clavel & Morlon (2020) <DOI:10.1093/sysbio/syaa010>.
Maintained by Julien Clavel. Last updated 2 months ago.
3.5 match 17 stars 9.46 score 189 scripts 3 dependents
matthieu-bruneaux
isotracer:Isotopic Tracer Analysis Using MCMC
Implements Bayesian models to analyze data from tracer addition experiments. The implemented method was originally described in the article "A New Method to Reconstruct Quantitative Food Webs and Nutrient Flows from Isotope Tracer Addition Experiments" by López-Sepulcre et al. (2020) <doi:10.1086/708546>.
Maintained by Matthieu Bruneaux. Last updated 5 months ago.
5.3 match 5.92 score 60 scripts
tjaki
PK:Basic Non-Compartmental Pharmacokinetics
Estimation of pharmacokinetic parameters using non-compartmental theory.
Maintained by Thomas Jaki. Last updated 2 years ago.
10.3 match 2.59 score 13 scripts 1 dependents
r-spark
sparklyr.flint:Sparklyr Extension for 'Flint'
This sparklyr extension makes 'Flint' time series library functionalities (<https://github.com/twosigma/flint>) easily accessible through R.
Maintained by Edgar Ruiz. Last updated 3 years ago.
apache-sparkdata-analysisdata-miningdata-sciencedistributeddistributed-computingflintremote-clusterssparksparklyrstatistical-analysisstatisticsstatssummarizationsummary-statisticstime-seriestime-series-analysistwosigma-flint
3.8 match 9 stars 6.46 score 54 scripts
huismanj
qpNCA:Noncompartmental Pharmacokinetic Analysis by qPharmetra
Computes noncompartmental pharmacokinetic parameters for drug concentration profiles. For each profile, data imputations and adjustments are made as necessary and basic parameters are estimated. Supports single dose, multi-dose, and multi-subject data. Supports steady-state calculations and various routes of drug administration. See ?qpNCA and vignettes. Methodology follows Rowland and Tozer (2011, ISBN:978-0-683-07404-8), Gabrielsson and Weiner (1997, ISBN:978-91-9765-100-4), and Gibaldi and Perrier (1982, ISBN:978-0824710422).
Maintained by Jan Huisman. Last updated 4 years ago.
6.1 match 3.83 score 34 scripts
reckziegel
ffp:Fully Flexible Probabilities for Stress Testing and Portfolio Construction
Implements numerical entropy-pooling for portfolio construction and scenario analysis as described in Meucci, Attilio (2008) and Meucci, Attilio (2010) <doi:10.2139/ssrn.1696802>.
Maintained by Bernardo Reckziegel. Last updated 3 years ago.
bayesian-inferenceentropy-poolingflexible-probabilitiesportolio-optimizationrisk-managementscenariosviews
4.0 match 16 stars 5.71 score 32 scripts
benjaminrich
linpk:Generate Concentration-Time Profiles from Linear PK Systems
Generate concentration-time profiles from linear pharmacokinetic (PK) systems, possibly with first-order absorption or zero-order infusion, possibly with one or more peripheral compartments, and possibly under steady-state conditions. Single or multiple doses may be specified. Secondary (derived) PK parameters (e.g. Cmax, Ctrough, AUC, Tmax, half-life, etc.) are computed.
Maintained by Benjamin Rich. Last updated 12 months ago.
4.3 match 10 stars 4.90 score 16 scripts
kwb-r
kwb.fcr:Fertilizer chemical risk assessment
This risk assessment is based on the TGD on risk assessment by the European Comission. Possible Endpoints are soil organisms, groundwater organisms and human health via food consumption.Every variable can be entered as probability distribution to include uncertainties or site specific variations.
Maintained by Malte Zamzow. Last updated 1 years ago.
3.8 match 3.00 score 2 scripts
cran
REAT:Regional Economic Analysis Toolbox
Collection of models and analysis methods used in regional and urban economics and (quantitative) economic geography, e.g. measures of inequality, regional disparities and convergence, regional specialization as well as accessibility and spatial interaction models.
Maintained by Thomas Wieland. Last updated 4 years ago.
3.4 match 3 stars 2.48 scorecran
Inquilab:Dissipation Kinetics Analysis, Half Life Period, Rate Constant, Plots
For environmental chemists, ecologists, researchers and agricultural scientists to understand the dissipation kinetics, calculate the half-life periods and rate constants of compounds, pesticides, contaminants in different matrices.
Maintained by Jajati Mandal. Last updated 1 years ago.
6.6 match 1.00 scorebioc
rifiComparative:'rifiComparative' compares the output of rifi from two different conditions.
'rifiComparative' is a continuation of rifi package. It compares two conditions output of rifi using half-life and mRNA at time 0 segments. As an input for the segmentation, the difference between half-life of both condtions and log2FC of the mRNA at time 0 are used. The package provides segmentation, statistics, summary table, fragments visualization and some additional useful plots for further anaylsis.
Maintained by Loubna Youssar. Last updated 5 months ago.
rnaseqdifferentialexpressiongeneregulationtranscriptomicsmicroarraysoftware
1.6 match 4.00 score
bioc
RNAdecay:Maximum Likelihood Decay Modeling of RNA Degradation Data
RNA degradation is monitored through measurement of RNA abundance after inhibiting RNA synthesis. This package has functions and example scripts to facilitate (1) data normalization, (2) data modeling using constant decay rate or time-dependent decay rate models, (3) the evaluation of treatment or genotype effects, and (4) plotting of the data and models. Data Normalization: functions and scripts make easy the normalization to the initial (T0) RNA abundance, as well as a method to correct for artificial inflation of Reads per Million (RPM) abundance in global assessments as the total size of the RNA pool decreases. Modeling: Normalized data is then modeled using maximum likelihood to fit parameters. For making treatment or genotype comparisons (up to four), the modeling step models all possible treatment effects on each gene by repeating the modeling with constraints on the model parameters (i.e., the decay rate of treatments A and B are modeled once with them being equal and again allowing them to both vary independently). Model Selection: The AICc value is calculated for each model, and the model with the lowest AICc is chosen. Modeling results of selected models are then compiled into a single data frame. Graphical Plotting: functions are provided to easily visualize decay data model, or half-life distributions using ggplot2 package functions.
Maintained by Reed Sorenson. Last updated 5 months ago.
immunooncologysoftwaregeneexpressiongeneregulationdifferentialexpressiontranscriptiontranscriptomicstimecourseregressionrnaseqnormalizationworkflowstep
1.0 match 4.18 score 2 scripts