Package: SeqFeatR 0.3.1

Bettina Budeus

SeqFeatR: A Tool to Associate FASTA Sequences and Features

Provides user friendly methods for the identification of sequence patterns that are statistically significantly associated with a property of the sequence. For instance, SeqFeatR allows to identify viral immune escape mutations for hosts of given HLA types. The underlying statistical method is Fisher's exact test, with appropriate corrections for multiple testing, or Bayes. Patterns may be point mutations or n-tuple of mutations. SeqFeatR offers several ways to visualize the results of the statistical analyses, see Budeus (2016) <doi:10.1371/journal.pone.0146409>.

Authors:Bettina Budeus

SeqFeatR_0.3.1.tar.gz
SeqFeatR_0.3.1.tar.gz(r-4.5-noble)SeqFeatR_0.3.1.tar.gz(r-4.4-noble)
SeqFeatR_0.3.1.tgz(r-4.4-emscripten)SeqFeatR_0.3.1.tgz(r-4.3-emscripten)
SeqFeatR.pdf |SeqFeatR.html✨
SeqFeatR/json (API)
NEWS

# Install 'SeqFeatR' in R:

install.packages('SeqFeatR', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Uses libs:

jags– Just Another Gibbs Sampler for Bayesian MCMC
c++– GNU Standard C++ Library v3

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

jags cpp

2.30 score 357 downloads 2 mentions 18 exports 68 dependencies

Last updated 6 years agofrom:fc9916d2d3. Checks:2 OK. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Feb 24 2025
R-4.5-linux	OK	Feb 24 2025

Exports:assocpair assocpairfeat assocpoint assocpointhierarchical assocpointpair assoctuple comparewithancestral foundereffectfinder getfreqs orPlot qvalues rewritetuple SeqFeatR_GUI smallmanhattan tartan visualizepair visualizepairfeat volcanoplot

Dependencies:abind ape askpass BiocGenerics Biostrings boot calibrate cli coda colorspace cpp11 crayon curl digest fansi farver fastmatch generics GenomeInfoDb GenomeInfoDbData ggplot2 glue gtable httr igraph IRanges isoband jsonlite labeling lattice lifecycle magrittr MASS Matrix mgcv mime munsell nlme openssl phangorn pillar pkgconfig plotrix plyr quadprog qvalue R2jags R2WinBUGS R6 RColorBrewer Rcpp reshape2 rjags rlang S4Vectors scales stringi stringr sys tcltk2 tibble UCSC.utils utf8 vctrs viridisLite widgetTools withr XVector

SeqFeatR Tutorial

Rendered fromSeqFeatR_tutorial.Rnwusingutils::Sweaveon Feb 24 2025.

Last update: 2018-03-06
Started: 2015-02-10

Help page	Topics
Finding pairs of alignment positions that jointly mutate	assocpair
Finding pairs of sequence alignment positions associated with sequence feature.	assocpairfeat
Searches for associations of single alignment positions with feature(s)	assocpoint
Searches for associations of single alignment positions with feature(s) with a simple hierarchical model	assocpointhierarchical
Compare results of SeqFeatRs assocpoint with SeqFeatRs assocpair, assocpairfeat	assocpointpair
Searches for associations of a tuple of alignment positions with feature(s)	assoctuple
Compares ancestral sequence with sequence alignment	comparewithancestral
Tries to identify a founder effect in results from SeqFeatRs assocpair	foundereffectfinder
Get frequencies for amino acids/nucleotides in alignment window (epitope)	getfreqs
Visualize odds ratios and p-values from SeqFeatRs assocpoint	orPlot
Calculate q-values from p-values	qvalues
Rewrite result from SeqFeatRs assoctuple	rewritetuple
GUI for SeqFeatR	SeqFeatR_GUI
A small version of manhattan plot	smallmanhattan
Visualize association of mutation pairs and features from two (comparable) analyses.	tartan
Visualize pairs of alignment positions that jointly mutate	visualizepair
Visualize pairs of sequence alignment positions associated with sequence feature.	visualizepairfeat
Create volcano plot	volcanoplot

Package: SeqFeatR 0.3.1

SeqFeatR: A Tool to Associate FASTA Sequences and Features

SeqFeatR Tutorial

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)