signalHsmm: Predict Presence of Signal Peptides

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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.

Author
Michal Burdukiewicz [cre, aut], Piotr Sobczyk [aut]
Date of publication
2016-03-03 14:16:37
Maintainer
Michal Burdukiewicz <michalburdukiewicz@gmail.com>
License
GPL-3
Version
1.4
URLs

View on CRAN

Man pages

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

Files in this package

signalHsmm
signalHsmm/inst
signalHsmm/inst/CITATION
signalHsmm/inst/signal_gui
signalHsmm/inst/signal_gui/ui.R
signalHsmm/inst/signal_gui/server.R
signalHsmm/inst/signal_gui/readme.md
signalHsmm/inst/signal_gui/logo.png
signalHsmm/inst/signal_gui/prots.txt
signalHsmm/inst/signal_gui/signalhsmm_report.Rmd
signalHsmm/src
signalHsmm/src/duration_viterbi.cpp
signalHsmm/src/RcppExports.cpp
signalHsmm/NAMESPACE
signalHsmm/CHANGELOG
signalHsmm/data
signalHsmm/data/benchmark_dat.rda
signalHsmm/data/aaaggregation.rda
signalHsmm/R
signalHsmm/R/add_k_mer_state.R
signalHsmm/R/utils.R
signalHsmm/R/hsmm_pred.R
signalHsmm/R/read_txt.R
signalHsmm/R/run_signalHsmm.R
signalHsmm/R/read_uniprot.R
signalHsmm/R/signalHsmm.R
signalHsmm/R/RcppExports.R
signalHsmm/R/predict.sighsmm_model.R
signalHsmm/R/find_nhc.R
signalHsmm/R/train_hsmm.R
signalHsmm/R/is_protein.R
signalHsmm/R/datasets.R
signalHsmm/R/hsmm_pred_list.R
signalHsmm/R/sighsmm_model.R
signalHsmm/README.md
signalHsmm/MD5
signalHsmm/DESCRIPTION
signalHsmm/man
signalHsmm/man/duration_viterbi.Rd
signalHsmm/man/benchmark_dat.Rd
signalHsmm/man/gui_signalHsmm.Rd
signalHsmm/man/predict.sighsmm_model.Rd
signalHsmm/man/hsmm_pred_list.Rd
signalHsmm/man/run_signalHsmm.Rd
signalHsmm/man/hsmm_pred.Rd
signalHsmm/man/signalHsmm.Rd
signalHsmm/man/train_hsmm.Rd
signalHsmm/man/is_protein.Rd
signalHsmm/man/add_k_mer_state.Rd
signalHsmm/man/summary.hsmm_pred.Rd
signalHsmm/man/read_uniprot.Rd
signalHsmm/man/summary.hsmm_pred_list.Rd
signalHsmm/man/pred2df.Rd
signalHsmm/man/find_nhc.Rd
signalHsmm/man/read_txt.Rd
signalHsmm/man/aaaggregation.Rd
signalHsmm/man/plot.hsmm_pred.Rd