Showing 8 of total 8 results (show query)
kkholst
lava:Latent Variable Models
A general implementation of Structural Equation Models with latent variables (MLE, 2SLS, and composite likelihood estimators) with both continuous, censored, and ordinal outcomes (Holst and Budtz-Joergensen (2013) <doi:10.1007/s00180-012-0344-y>). Mixture latent variable models and non-linear latent variable models (Holst and Budtz-Joergensen (2020) <doi:10.1093/biostatistics/kxy082>). The package also provides methods for graph exploration (d-separation, back-door criterion), simulation of general non-linear latent variable models, and estimation of influence functions for a broad range of statistical models.
Maintained by Klaus K. Holst. Last updated 3 months ago.
latent-variable-modelssimulationstatisticsstructural-equation-models
33 stars 12.87 score 610 scripts 478 dependents
bioc
musicatk:Mutational Signature Comprehensive Analysis Toolkit
Mutational signatures are carcinogenic exposures or aberrant cellular processes that can cause alterations to the genome. We created musicatk (MUtational SIgnature Comprehensive Analysis ToolKit) to address shortcomings in versatility and ease of use in other pre-existing computational tools. Although many different types of mutational data have been generated, current software packages do not have a flexible framework to allow users to mix and match different types of mutations in the mutational signature inference process. Musicatk enables users to count and combine multiple mutation types, including SBS, DBS, and indels. Musicatk calculates replication strand, transcription strand and combinations of these features along with discovery from unique and proprietary genomic feature associated with any mutation type. Musicatk also implements several methods for discovery of new signatures as well as methods to infer exposure given an existing set of signatures. Musicatk provides functions for visualization and downstream exploratory analysis including the ability to compare signatures between cohorts and find matching signatures in COSMIC V2 or COSMIC V3.
Maintained by Joshua D. Campbell. Last updated 5 months ago.
softwarebiologicalquestionsomaticmutationvariantannotation
13 stars 6.97 score 20 scriptsbioc
isobar:Analysis and quantitation of isobarically tagged MSMS proteomics data
isobar provides methods for preprocessing, normalization, and report generation for the analysis of quantitative mass spectrometry proteomics data labeled with isobaric tags, such as iTRAQ and TMT. Features modules for integrating and validating PTM-centric datasets (isobar-PTM). More information on http://www.ms-isobar.org.
Maintained by Florian P Breitwieser. Last updated 5 months ago.
immunooncologyproteomicsmassspectrometrybioinformaticsmultiplecomparisonsqualitycontrol
10 stars 6.96 score 19 scripts
dynverse
dynparam:Creating Meta-Information for Parameters
Provides tools for describing parameters of algorithms in an abstract way. Description can include an id, a description, a domain (range or list of values), and a default value. 'dynparam' can also convert parameter sets to a 'ParamHelpers' format, in order to be able to use 'dynparam' in conjunction with 'mlrMBO'.
Maintained by Robrecht Cannoodt. Last updated 6 years ago.
2 stars 3.95 score 15 scripts 2 dependentsbioc
rqubic:Qualitative biclustering algorithm for expression data analysis in R
This package implements the QUBIC algorithm introduced by Li et al. for the qualitative biclustering with gene expression data.
Maintained by Jitao David Zhang. Last updated 5 months ago.
3.78 score 4 scripts 1 dependents
cran
ips:Interfaces to Phylogenetic Software in R
Functions that wrap popular phylogenetic software for sequence alignment, masking of sequence alignments, and estimation of phylogenies and ancestral character states.
Maintained by Christoph Heibl. Last updated 11 months ago.
3.18 score 1 dependents
bachfisch
PHENTHAUproc:Phenology Modelling of Thaumetopoea Processionea
Methods to calculate and present 'PHENTHAUproc', an early warning and decision support system for hazard assessment and control of oak processionary moth (OPM) using local and spatial temperature data. It was created by Halbig et al. 2024 (<doi:10.1016/j.foreco.2023.121525>) at FVA (<https://www.fva-bw.de/en/homepage/>) Forest Research Institute Baden-Wuerttemberg, Germany and at BOKU - University of Natural Ressources and Life Sciences, Vienna, Austria.
Maintained by Lorenz Bachfischer. Last updated 10 months ago.
2.70 score 3 scripts
