Package: signalHsmm 1.5

signalHsmm: Predict Presence of Signal Peptides

Predicts the presence of signal peptides in eukaryotic protein using hidden semi-Markov models. The implemented algorithm can be accessed from both the command line and GUI.

Authors:Michal Burdukiewicz [cre, aut], Piotr Sobczyk [aut], Jaroslaw Chilimoniuk [ctb]

signalHsmm_1.5.tar.gz
signalHsmm_1.5.zip(r-4.5)signalHsmm_1.5.zip(r-4.4)signalHsmm_1.5.zip(r-4.3)
signalHsmm_1.5.tgz(r-4.4-x86_64)signalHsmm_1.5.tgz(r-4.4-arm64)signalHsmm_1.5.tgz(r-4.3-x86_64)signalHsmm_1.5.tgz(r-4.3-arm64)
signalHsmm_1.5.tar.gz(r-4.5-noble)signalHsmm_1.5.tar.gz(r-4.4-noble)
signalHsmm_1.5.tgz(r-4.4-emscripten)signalHsmm_1.5.tgz(r-4.3-emscripten)
signalHsmm.pdf |signalHsmm.html✨
signalHsmm/json (API)

# Install 'signalHsmm' in R:

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

Bug tracker:https://github.com/michbur/signalhsmm/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

aaaggregation - Reduced amino acid alphabet
benchmark_dat - Benchmark data set for signalHsmm

On CRAN:

10 exports 2 stars 1.32 score 39 dependencies 1 mentions 7 scripts 139 downloads

Last updated 4 years agofrom:7a9a3a7236. Checks:OK: 4 NOTE: 5. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 04 2024
R-4.5-win-x86_64	NOTE	Sep 04 2024
R-4.5-linux-x86_64	NOTE	Sep 04 2024
R-4.4-win-x86_64	NOTE	Sep 04 2024
R-4.4-mac-x86_64	NOTE	Sep 04 2024
R-4.4-mac-aarch64	NOTE	Sep 04 2024
R-4.3-win-x86_64	OK	Sep 04 2024
R-4.3-mac-x86_64	OK	Sep 04 2024
R-4.3-mac-aarch64	OK	Sep 04 2024

Exports:add_k_mer_state duration_viterbi find_nhc gui_signalHsmm is_protein pred2df read_txt read_uniprot run_signalHsmm train_hsmm

Dependencies:ade4 base64enc bslib cachem cli commonmark crayon digest fastmap fontawesome fs glue htmltools httpuv jquerylib jsonlite later lattice lifecycle magrittr MASS memoise mime nlme pixmap promises R6 rappdirs Rcpp RcppArmadillo rlang sass segmented seqinr shiny sourcetools sp withr xtable

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Reduced amino acid alphabet	aaaggregation
Adds k-mer hidden state to signalHsmm model	add_k_mer_state
Benchmark data set for signalHsmm	benchmark_dat
Compute most probable path with extended Viterbi algorithm.	duration_viterbi
Localize n-, h- and c-region in signal peptide	find_nhc
GUI for signalHsmm	gui_signalHsmm
hsmm_pred class	hsmm_pred
hsmm_pred_list class	hsmm_pred_list
Protein test	is_protein
Plot single signalHsmm prediction	plot.hsmm_pred
Convert list of signalHsmm predictions	pred2df
Predict sighsmm_model object	predict.sighsmm_model
Read sequences from .txt file	read_txt
Read data from UniProt database	read_uniprot
Predict presence of signal peptide in protein	run_signalHsmm
signalHsmm - prediction of signal peptides	signalHsmm-package signalHsmm
Summarize single signalHsmm prediction	summary.hsmm_pred
Summarize list of signalHsmm predictions	summary.hsmm_pred_list
Train sighsmm_model object	train_hsmm