Showing 25 of total 25 results (show query)
ocbe-uio
BayesMallows:Bayesian Preference Learning with the Mallows Rank Model
An implementation of the Bayesian version of the Mallows rank model (Vitelli et al., Journal of Machine Learning Research, 2018 <https://jmlr.org/papers/v18/15-481.html>; Crispino et al., Annals of Applied Statistics, 2019 <doi:10.1214/18-AOAS1203>; Sorensen et al., R Journal, 2020 <doi:10.32614/RJ-2020-026>; Stein, PhD Thesis, 2023 <https://eprints.lancs.ac.uk/id/eprint/195759>). Both Metropolis-Hastings and sequential Monte Carlo algorithms for estimating the models are available. Cayley, footrule, Hamming, Kendall, Spearman, and Ulam distances are supported in the models. The rank data to be analyzed can be in the form of complete rankings, top-k rankings, partially missing rankings, as well as consistent and inconsistent pairwise preferences. Several functions for plotting and studying the posterior distributions of parameters are provided. The package also provides functions for estimating the partition function (normalizing constant) of the Mallows rank model, both with the importance sampling algorithm of Vitelli et al. and asymptotic approximation with the IPFP algorithm (Mukherjee, Annals of Statistics, 2016 <doi:10.1214/15-AOS1389>).
Maintained by Oystein Sorensen. Last updated 1 months ago.
mallows-modelopenblascppopenmp
15.0 match 21 stars 7.91 score 36 scripts 1 dependents
lcbc-uio
galamm:Generalized Additive Latent and Mixed Models
Estimates generalized additive latent and mixed models using maximum marginal likelihood, as defined in Sorensen et al. (2023) <doi:10.1007/s11336-023-09910-z>, which is an extension of Rabe-Hesketh and Skrondal (2004)'s unifying framework for multilevel latent variable modeling <doi:10.1007/BF02295939>. Efficient computation is done using sparse matrix methods, Laplace approximation, and automatic differentiation. The framework includes generalized multilevel models with heteroscedastic residuals, mixed response types, factor loadings, smoothing splines, crossed random effects, and combinations thereof. Syntax for model formulation is close to 'lme4' (Bates et al. (2015) <doi:10.18637/jss.v067.i01>) and 'PLmixed' (Rockwood and Jeon (2019) <doi:10.1080/00273171.2018.1516541>).
Maintained by Øystein Sørensen. Last updated 6 months ago.
generalized-additive-modelshierarchical-modelsitem-response-theorylatent-variable-modelsstructural-equation-modelscpp
15.0 match 29 stars 7.33 score 41 scripts
capro-uio
uiothemes:Branding themes for the University of Oslo, Norway
Contains templates, themeing files and functions. Made specifically for branding purposes for the University of Oslo.
Maintained by Athanasia Mo Mowinckel. Last updated 4 years ago.
35.3 match 14 stars 2.85 score 2 scriptscapro-uio
nettskjemar:Connect to the 'nettskjema.no' API of the University of Oslo
Enables users to retrieve data, meta-data, and codebooks from <https://nettskjema.no/>. The data from the API is richer than from the online data portal. Mowinckel (2021) <doi:10.5281/zenodo.4745481>.
Maintained by Athanasia Mo Mowinckel. Last updated 8 hours ago.
15.0 match 2 stars 5.29 score 14 scriptslcbc-uio
tsdrtools:Convenience package for installing R-packages on UiO TSD
Some packages are hard to install on the secure closed server of the University of Oslo, TSD This package has some functions to help users more easily install packages to TSD that cannot be installed using the mini-CRAN service within TSD.
Maintained by Athanasia Mo Mowinckel. Last updated 3 years ago.
17.9 match 6 stars 4.18 score 5 scriptscapro-uio
tsdrtools:Convenience package for installing R-packages on UiO TSD
Some packages are hard to install on the secure closed server of the University of Oslo, TSD This package has some functions to help users more easily install packages to TSD that cannot be installed using the mini-CRAN service within TSD.
Maintained by Athanasia Mo Mowinckel. Last updated 3 years ago.
17.9 match 6 stars 4.18 score 5 scriptsocbe-uio
TruncExpFam:Truncated Exponential Family
Handles truncated members from the exponential family of probability distributions. Contains functions such as rtruncnorm() and dtruncpois(), which are truncated versions of rnorm() and dpois() from the stats package that also offer richer output containing, for example, the distribution parameters. It also provides functions to retrieve the original distribution parameters from a truncated sample by maximum-likelihood estimation.
Maintained by Waldir Leoncio. Last updated 6 months ago.
15.0 match 4.85 score 6 scriptsocbe-uio
BayesSurvive:Bayesian Survival Models for High-Dimensional Data
An implementation of Bayesian survival models with graph-structured selection priors for sparse identification of omics features predictive of survival (Madjar et al., 2021 <doi:10.1186/s12859-021-04483-z>) and its extension to use a fixed graph via a Markov Random Field (MRF) prior for capturing known structure of omics features, e.g. disease-specific pathways from the Kyoto Encyclopedia of Genes and Genomes database.
Maintained by Zhi Zhao. Last updated 6 months ago.
bayesian-cox-modelsbayesian-variable-selectiongraph-learninghigh-dimensional-statisticsomics-data-integrationsurvival-analysiscpp
15.0 match 1 stars 4.70 score 1 scriptsocbe-uio
psbcSpeedUp:Penalized Semiparametric Bayesian Cox Models
Algorithms to speed up the Bayesian Lasso Cox model (Lee et al., Int J Biostat, 2011 <doi:10.2202/1557-4679.1301>) and the Bayesian Lasso Cox with mandatory variables (Zucknick et al. Biometrical J, 2015 <doi:10.1002/bimj.201400160>).
Maintained by Zhi Zhao. Last updated 9 months ago.
bayesian-cox-modelsomics-datasurvival-analysisopenblascppopenmp
15.0 match 3 stars 4.65 scorelcbc-uio
questionnaires:Package with functions to calculate components and sums for LCBC questionnaires
Creates summaries and factorials of answers to questionnaires.
Maintained by Athanasia Mo Mowinckel. Last updated 2 years ago.
15.0 match 3 stars 4.63 score 13 scriptsocbe-uio
EnrichIntersect:Enrichment Analysis and Intersecting Sankey Diagram
A flexible tool for enrichment analysis based on user-defined sets. It allows users to perform over-representation analysis of the custom sets among any specified ranked feature list, hence making enrichment analysis applicable to various types of data from different scientific fields. 'EnrichIntersect' also enables an interactive means to visualize identified associations based on, for example, the mix-lasso model (Zhao et al., 2022 <doi:10.1016/j.isci.2022.104767>) or similar methods.
Maintained by Zhi Zhao. Last updated 12 months ago.
15.0 match 4 stars 4.60 scoreocbe-uio
DIscBIO:A User-Friendly Pipeline for Biomarker Discovery in Single-Cell Transcriptomics
An open, multi-algorithmic pipeline for easy, fast and efficient analysis of cellular sub-populations and the molecular signatures that characterize them. The pipeline consists of four successive steps: data pre-processing, cellular clustering with pseudo-temporal ordering, defining differential expressed genes and biomarker identification. More details on Ghannoum et. al. (2021) <doi:10.3390/ijms22031399>. This package implements extensions of the work published by Ghannoum et. al. (2019) <doi:10.1101/700989>.
Maintained by Waldir Leoncio. Last updated 1 years ago.
biomarker-discoveryjupyter-notebookscrna-seqsingle-cell-analysistranscriptomicsopenjdk
15.0 match 12 stars 4.38 score 5 scriptsocbe-uio
permChacko:Chacko Test for Order-Restriction with Permutation
Implements an extension of the Chacko chi-square test for ordered vectors (Chacko, 1966, <https://www.jstor.org/stable/25051572>). Our extension brings the Chacko test to the computer age by implementing a permutation test to offer a numeric estimate of the p-value, which is particularly useful when the analytic solution is not available.
Maintained by Waldir Leoncio. Last updated 6 months ago.
15.0 match 4.30 score 3 scriptsocbe-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.
15.0 match 3 stars 4.13 score 8 scripts 1 dependents
drmowinckels
uiothemes:Branding themes for the University of Oslo, Norway
Contains templates, themeing files and functions. Made specifically for branding purposes for the University of Oslo.
Maintained by Athanasia Mo Mowinckel. Last updated 4 years ago.
20.3 match 14 stars 2.85 score 2 scriptslcbc-uio
Conversions:Collection of functions that convert certain RAW data in the LCBC database
Collection of functions that convert certain RAW data in the LCBC database.
Maintained by Athanasia Monika Mowinckel. Last updated 4 years ago.
15.0 match 3.65 score 10 scriptsocbe-uio
matlab2r:Translation Layer from MATLAB to R
Allows users familiar with MATLAB to use MATLAB-named functions in R. Several basic MATLAB functions are written in this package to mimic the behavior of their original counterparts, with more to come as this package grows.
Maintained by Waldir Leoncio. Last updated 2 years ago.
15.0 match 2 stars 3.48 score 1 dependentslcbc-uio
noasr:NOAS convenience functions
Functions created to work well with LCBC's Nephew of All Spreadsheet data.
Maintained by Athanasia Mo Mowinckel. Last updated 4 years ago.
15.0 match 3.00 score 4 scriptslcbc-uio
lcbcr:LCBC brand package
Functions and setups with brand styling and lab general setups.
Maintained by Athanasia Mo Mowinckel. Last updated 3 years ago.
15.0 match 3.00 score 2 scriptslcbc-uio
nettskjema.tsd:Decrypt and Organise Nettskjema Data Within TSD
Working with Nettskjema (<https://nettskjema.no/>) data inside TSD can be challenging. This package aims to aid users in managing their incoming Nettskjema data by decrypting the data and storing the nettskjema data and meta-data in convenient and standardised ways. This package functionality currently only works on the Linux VMs of TSD, and for version 1 of the nettskjema data delivery to TSD.
Maintained by Athanasia Mo Mowinckel. Last updated 3 years ago.
15.0 match 2.70 score 3 scriptslcbc-uio
BayesianLaterality:Predict Brain Asymmetry Based on Handedness and Dichotic Listening
Functional differences between the cerebral hemispheres are a fundamental characteristic of the human brain. Researchers interested in studying these differences often infer underlying hemispheric dominance for a certain function (e.g., language) from laterality indices calculated from observed performance or brain activation measures . However, any inference from observed measures to latent (unobserved) classes has to consider the prior probability of class membership in the population. The provided functions implement a Bayesian model for predicting hemispheric dominance from observed laterality indices (Sorensen and Westerhausen, Laterality: Asymmetries of Body, Brain and Cognition, 2020, <doi:10.1080/1357650X.2020.1769124>).
Maintained by Oystein Sorensen. Last updated 2 years ago.
15.0 match 2.70 score 3 scriptscapro-uio
neuromat:Create Model Matrices for Neuroimaging Analyses
Neuroimaging software often requires the specification of model matrices to run analyses. These can be difficult to correctly. This package helps neuroscientists to create such This includes creating qdec-files for Freesurfer Linear Mixes Effects models.
Maintained by Athanasia Mo Mowinckel. Last updated 1 years ago.
15.0 match 2.70 score 2 scriptslcbc-uio
eprimeParser:LCBC E-prime data processing pipeline
This package contains functions to process the eprime data for LCBC. The functions are adaptations of scripts James Michael Roe made, that Athanasia Monika Mowinckel converted.
Maintained by Athanasia Mo Mowinckel. Last updated 5 years ago.
15.0 match 1.70 score 1 scriptslcbc-uio
psykinematix:Utilities to work with data from Psykinematix Visual Psychophysics
Psykinematix Visual Psychophysics is a tool to develop and deploy psychophysical experiments. This packages enables the user to read in data from this tool into R for further processing.
Maintained by Athanasia Mo Mowinckel. Last updated 3 years ago.
15.0 match 1.70 score 3 scripts
palryalen
ahw:Calculates Continuous Time Likelihood Ratio Weights Assuming Multiplicative Intensity Models and Additive Hazard Models
Estimates continuous time weights for performing causal survival analysis. For instance, weighted Nelson-Aalen or Kaplan-Meier estimates can be given a causal interpretation. See Ryalen, Stensrud, and Røysland (2019) <doi:10.1007/s10985-019-09468-y> and Ryalen (2019) <https://www.duo.uio.no/handle/10852/70353> for theory and examples.
Maintained by Pål Christie Ryalen. Last updated 2 years ago.
0.5 match 1.00 score