Showing 15 of total 15 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
jtextor
dagitty:Graphical Analysis of Structural Causal Models
A port of the web-based software 'DAGitty', available at <https://dagitty.net>, for analyzing structural causal models (also known as directed acyclic graphs or DAGs). This package computes covariate adjustment sets for estimating causal effects, enumerates instrumental variables, derives testable implications (d-separation and vanishing tetrads), generates equivalent models, and includes a simple facility for data simulation.
Maintained by Johannes Textor. Last updated 4 months ago.
302 stars 12.83 score 1.7k scripts 11 dependents
fmichonneau
phylobase:Base Package for Phylogenetic Structures and Comparative Data
Provides a base S4 class for comparative methods, incorporating one or more trees and trait data.
Maintained by Francois Michonneau. Last updated 1 years ago.
18 stars 11.10 score 394 scripts 18 dependents
bioc
OmnipathR:OmniPath web service client and more
A client for the OmniPath web service (https://www.omnipathdb.org) and many other resources. It also includes functions to transform and pretty print some of the downloaded data, functions to access a number of other resources such as BioPlex, ConsensusPathDB, EVEX, Gene Ontology, Guide to Pharmacology (IUPHAR/BPS), Harmonizome, HTRIdb, Human Phenotype Ontology, InWeb InBioMap, KEGG Pathway, Pathway Commons, Ramilowski et al. 2015, RegNetwork, ReMap, TF census, TRRUST and Vinayagam et al. 2011. Furthermore, OmnipathR features a close integration with the NicheNet method for ligand activity prediction from transcriptomics data, and its R implementation `nichenetr` (available only on github).
Maintained by Denes Turei. Last updated 1 months ago.
graphandnetworknetworkpathwayssoftwarethirdpartyclientdataimportdatarepresentationgenesignalinggeneregulationsystemsbiologytranscriptomicssinglecellannotationkeggcomplexesenzyme-ptmnetworksnetworks-biologyomnipathproteinsquarto
130 stars 9.90 score 226 scripts 2 dependents
hojsgaard
gRbase:A Package for Graphical Modelling in R
The 'gRbase' package provides graphical modelling features used by e.g. the packages 'gRain', 'gRim' and 'gRc'. 'gRbase' implements graph algorithms including (i) maximum cardinality search (for marked and unmarked graphs). (ii) moralization, (iii) triangulation, (iv) creation of junction tree. 'gRbase' facilitates array operations, 'gRbase' implements functions for testing for conditional independence. 'gRbase' illustrates how hierarchical log-linear models may be implemented and describes concept of graphical meta data. The facilities of the package are documented in the book by Højsgaard, Edwards and Lauritzen (2012, <doi:10.1007/978-1-4614-2299-0>) and in the paper by Dethlefsen and Højsgaard, (2005, <doi:10.18637/jss.v014.i17>). Please see 'citation("gRbase")' for citation details.
Maintained by Søren Højsgaard. Last updated 5 months ago.
3 stars 9.24 score 241 scripts 20 dependents
magnusdv
pedtools:Creating and Working with Pedigrees and Marker Data
A comprehensive collection of tools for creating, manipulating and visualising pedigrees and genetic marker data. Pedigrees can be read from text files or created on the fly with built-in functions. A range of utilities enable modifications like adding or removing individuals, breaking loops, and merging pedigrees. An online tool for creating pedigrees interactively, based on 'pedtools', is available at <https://magnusdv.shinyapps.io/quickped>. 'pedtools' is the hub of the 'pedsuite', a collection of packages for pedigree analysis. A detailed presentation of the 'pedsuite' is given in the book 'Pedigree Analysis in R' (Vigeland, 2021, ISBN:9780128244302).
Maintained by Magnus Dehli Vigeland. Last updated 12 days ago.
25 stars 8.72 score 60 scripts 18 dependentsbioc
rols:An R interface to the Ontology Lookup Service
The rols package is an interface to the Ontology Lookup Service (OLS) to access and query hundred of ontolgies directly from R.
Maintained by Laurent Gatto. Last updated 5 months ago.
immunooncologysoftwareannotationmassspectrometrygo
11 stars 8.30 score 89 scripts 5 dependentsbioc
ontoProc:processing of ontologies of anatomy, cell lines, and so on
Support harvesting of diverse bioinformatic ontologies, making particular use of the ontologyIndex package on CRAN. We provide snapshots of key ontologies for terms about cells, cell lines, chemical compounds, and anatomy, to help analyze genome-scale experiments, particularly cell x compound screens. Another purpose is to strengthen development of compelling use cases for richer interfaces to emerging ontologies.
Maintained by Vincent Carey. Last updated 17 days ago.
infrastructuregobioinformaticsgenomicsontology
3 stars 6.37 score 75 scripts 2 dependentsbioc
Pedixplorer:Pedigree Functions
Routines to handle family data with a Pedigree object. The initial purpose was to create correlation structures that describe family relationships such as kinship and identity-by-descent, which can be used to model family data in mixed effects models, such as in the coxme function. Also includes a tool for Pedigree drawing which is focused on producing compact layouts without intervention. Recent additions include utilities to trim the Pedigree object with various criteria, and kinship for the X chromosome.
Maintained by Louis Le Nezet. Last updated 15 days ago.
softwaredatarepresentationgeneticsgraphandnetworkvisualizationkinshippedigree
2 stars 6.08 score 10 scripts
anikoszabo
Oncotree:Estimating Oncogenetic Trees
Construct and evaluate directed tree structures that model the process of occurrence of genetic alterations during carcinogenesis as described in Szabo, A. and Boucher, K (2002) <doi:10.1016/S0025-5564(02)00086-X>.
Maintained by Aniko Szabo. Last updated 2 years ago.
4.28 score 19 scripts
lucaweihs
SEMID:Identifiability of Linear Structural Equation Models
Provides routines to check identifiability or non-identifiability of linear structural equation models as described in Drton, Foygel, and Sullivant (2011) <doi:10.1214/10-AOS859>, Foygel, Draisma, and Drton (2012) <doi:10.1214/12-AOS1012>, and other works. The routines are based on the graphical representation of structural equation models.
Maintained by Nils Sturma. Last updated 2 years ago.
4 stars 4.06 score 29 scripts
cran
Rdiagnosislist:Manipulate SNOMED CT Diagnosis Lists
Functions and methods for manipulating 'SNOMED CT' concepts. The package contains functions for loading the 'SNOMED CT' release into a convenient R environment, selecting 'SNOMED CT' concepts using regular expressions, and navigating the 'SNOMED CT' ontology. It provides the 'SNOMEDconcept' S3 class for a vector of 'SNOMED CT' concepts (stored as 64-bit integers) and the 'SNOMEDcodelist' S3 class for a table of concepts IDs with descriptions. The package can be used to construct sets of 'SNOMED CT' concepts for research (<doi:10.1093/jamia/ocac158>). For more information about 'SNOMED CT' visit <https://www.snomed.org/>.
Maintained by Anoop D. Shah. Last updated 2 months ago.
1 stars 3.60 score
