Package: biogram 1.6.3

biogram: N-Gram Analysis of Biological Sequences

Tools for extraction and analysis of various n-grams (k-mers) derived from biological sequences (proteins or nucleic acids). Contains QuiPT (quick permutation test) for fast feature-filtering of the n-gram data.

Authors:Michal Burdukiewicz [cre, aut], Piotr Sobczyk [aut], Chris Lauber [aut], Dominik Rafacz [aut], Katarzyna Sidorczuk [ctb]

biogram_1.6.3.tar.gz
biogram_1.6.3.zip(r-4.5)biogram_1.6.3.zip(r-4.4)biogram_1.6.3.zip(r-4.3)
biogram_1.6.3.tgz(r-4.4-any)biogram_1.6.3.tgz(r-4.3-any)
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biogram.pdf |biogram.html✨
biogram/json (API)

# Install 'biogram' in R:
install.packages('biogram', repos = c('https://michbur.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

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

Datasets:
  • aaprop - Normalized amino acids properties
  • human_cleave - Human signal peptides cleavage sites

On CRAN:

biological-sequencesngram-analysis

7.67 score 10 stars 3 packages 87 scripts 288 downloads 49 exports 13 dependencies

Last updated 3 months agofrom:c06cd55946. Checks:OK: 1 ERROR: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 29 2024
R-4.5-winERROROct 29 2024
R-4.5-linuxERROROct 29 2024
R-4.4-winERROROct 29 2024
R-4.4-macERROROct 29 2024
R-4.3-winERROROct 29 2024
R-4.3-macERROROct 29 2024

Exports:add_1gramsbinarizecalc_criterioncalc_cscalc_edcalc_igcalc_klcalc_picalc_sicheck_criterioncluster_reg_expcode_ngramsconstruct_ngramscount_multigramscount_ngramscount_specifiedcount_totalcreate_encodingcreate_feature_targetcreate_ngramsdecode_ngramsdegeneratedegenerate_ngramsdistr_critencoding2dffast_crosstablefull2simplegap_ngramsgenerate_single_regiongenerate_single_unigramgenerate_unigramsget_ngrams_indis_ngraml2nlengths_ngramslist2matrixn2lngrams2dfposition_ngramsread_fastaread_txtregenerateseq2ngramssimple2fulltable_ngramstest_featuresvalidate_encodingwrite_encodingwrite_fasta

Dependencies:combinatentropygmplatticemathjaxrMatrixpartitionspbapplypolynomrbibutilsRdpacksetsslam

biogram package

Michał Burdukiewicz, Piotr Sobczyk

Rendered fromoverview.Rmdusingknitr::rmarkdownon Oct 29 2024.

Last update: 2020-04-01
Started: 2015-10-29

Readme and manuals

Help Manual

Help pageTopics
biogram - analysis of biological sequences using n-gramsbiogram-package biogram
Normalized amino acids propertiesaaprop
Add 1-gramsadd_1grams
Coerce feature_test object to a data frameas.data.frame.feature_test
Binarizebinarize
Calculate value of criterioncalc_criterion
Calculate Chi-squared-based measurecalc_cs
Calculate encoding distancecalc_ed
Calculate IG for single featurecalc_ig
Calculate KL divergence of featurescalc_kl
Calculate partition indexcalc_pi
Compute similarity indexcalc_si
Check chosen criterioncheck_criterion
Clustering of sequences based on regular expressioncluster_reg_exp
Code n-gramscode_ngrams
Construct and filter n-gramsconstruct_ngrams
Detect and count multiple n-grams in sequencescount_multigrams
Count n-grams in sequencescount_ngrams
Count specified n-gramscount_specified
Count total number of n-gramscount_total
Create encodingcreate_encoding
Create feature according to given contingency matrixcreate_feature_target
Get all possible n-Gramscreate_ngrams
criterion_distribution classcriterion_distribution
Categorize tested featurescut.feature_test
Decode n-gramsdecode_ngrams
Degenerate protein sequencedegenerate
Degenerate n-gramsdegenerate_ngrams
Compute criterion distributiondistr_crit
Convert encoding to data frameencoding2df
2d cross-tabulationfast_crosstable
feature_test classfeature_test
Convert encoding from full to simple formatfull2simple
Gap n-gramsgap_ngrams
Generate sequencegenerate_sequence
Generate single regiongenerate_single_region
Generate single unigramgenerate_single_unigram
Generate unigramsgenerate_unigrams
Get indices of n-gramsget_ngrams_ind
Human signal peptides cleavage siteshuman_cleave
Validate n-gramis_ngram
Convert letters to numbersl2n
Get lengths of the n-gramslengths_ngrams
Convert list of sequences to matrixlist2matrix
Convert numbers to lettersn2l
n-grams to data framengrams2df
Plot criterion distributionplot.criterion_distribution
Position n-gramsposition_ngrams
Print tested featuresprint.feature_test
Read FASTA filesread_fasta
Read sequences from .txt fileread_txt
Regenerate n-gramsregenerate
regional_param classregional_param
Extract n-grams from sequenceseq2ngrams
Convert encoding from simple to full formatsimple2full
Summarize tested featuressummary.feature_test
Tabulate n-gramstable_ngrams
Permutation test for feature selectiontest_features
Validate encodingvalidate_encoding
Write encodings to a filewrite_encoding
Write FASTA fileswrite_fasta