Other packages > Find by keyword >

aphid  

Analysis with Profile Hidden Markov Models
View on CRAN: Click here


Download and install aphid package within the R console
Install from CRAN:
install.packages("aphid")

Install from Github:
library("remotes")
install_github("cran/aphid")

Install by package version:
library("remotes")
install_version("aphid", "1.3.5")



Attach the package and use:
library("aphid")
Maintained by
Shaun Wilkinson
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2017-06-24
Latest Update: 2022-12-05
Description:
Designed for the development and application of hidden Markov models and profile HMMs for biological sequence analysis. Contains functions for multiple and pairwise sequence alignment, model construction and parameter optimization, file import/export, implementation of the forward, backward and Viterbi algorithms for conditional sequence probabilities, tree-based sequence weighting, and sequence simulation. Features a wide variety of potential applications including database searching, gene-finding and annotation, phylogenetic analysis and sequence classification. Based on the models and algorithms described in Durbin et al (1998, ISBN: 9780521629713).
How to cite:
Shaun Wilkinson (2017). aphid: Analysis with Profile Hidden Markov Models. R package version 1.3.5, https://cran.r-project.org/web/packages/aphid. Accessed 22 Dec. 2024.
Previous versions and publish date:
1.0.0 (2017-06-24 09:22), 1.0.1 (2017-07-07 12:14), 1.1.0 (2018-03-16 10:08), 1.2.0 (2018-08-14 11:50), 1.3.0 (2018-10-09 06:40), 1.3.1 (2018-11-10 06:50), 1.3.2 (2019-03-15 08:03), 1.3.3 (2019-05-08 07:20)
Other packages that cited aphid R package
View aphid citation profile
Other R packages that aphid depends, imports, suggests or enhances
Complete documentation for aphid
Functions, R codes and Examples using the aphid R package
Some associated functions: Viterbi . align . aphid . backward . casino . deriveHMM . derivePHMM . forward . generate . globins . logsum . map . plot.HMM . plot.PHMM . posterior . print . readPHMM . substitution . train . unalign . weight . writePHMM . 
Some associated R codes: RcppExports.R . Viterbi.R . align.R . aphid.R . backward.R . data.R . deriveHMM.R . derivePHMM.R . forward.R . generate.R . plot.R . posterior.R . print.R . read.R . train.R . utils.R . weight.R . write.R .  Full aphid package functions and examples
Downloads during the last 30 days
Get rewarded with contribution points by helping add
Reviews / comments / questions /suggestions ↴↴↴

Today's Hot Picks in Authors and Packages

Rfast2  
A Collection of Efficient and Extremely Fast R Functions II
A collection of fast statistical and utility functions for data analysis. Functions for regression, ...
Download / Learn more Package Citations See dependency  
composits  
Compositional, Multivariate and Univariate Time Series Outlier Ensemble
A compositional multivariate and univariate time series outlier ensemble.It uses the four R packages ...
Download / Learn more Package Citations See dependency  
dmlalg  
Double Machine Learning Algorithms
Implementation of double machine learning (DML) algorithms in R, based on Emmenegger and Buehlmann ...
Download / Learn more Package Citations See dependency  
LOGANTree  
Tree-Based Models for the Analysis of Log Files from Computer-Based Assessments
Enables researchers to model log-file data from computer-based assessments using machine-learning te ...
Download / Learn more Package Citations See dependency  
Maintainer: Qi Qin (view profile)
tropAlgebra  
Tropical Algebraic Functions
It includes functions like tropical addition, tropical multiplication for vectors and matrices. In t ...
Download / Learn more Package Citations See dependency  
elect  
Estimation of Life Expectancies Using Multi-State Models
Functions to compute state-specific and marginal life expectancies. The computation is based on a fi ...
Download / Learn more Package Citations See dependency  

23,394

R Packages

201,798

Dependencies

63,416

Author Associations

23,395

Publication Badges

© Copyright 2022 - present. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA