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biogram  

N-Gram Analysis of Biological Sequences
View on CRAN: Click here


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

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

Install by package version:
library("remotes")
install_version("biogram", "1.6.3")



Attach the package and use:
library("biogram")
Maintained by
Michal Burdukiewicz
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2014-12-19
Latest Update: 2020-03-31
Description:
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.
How to cite:
Michal Burdukiewicz (2014). biogram: N-Gram Analysis of Biological Sequences. R package version 1.6.3, https://cran.r-project.org/web/packages/biogram
Previous versions and publish date:
1.0 (2014-12-19 15:58), 1.1 (2015-02-03 11:18), 1.2 (2015-06-22 12:59), 1.3 (2016-09-21 12:21), 1.4 (2017-01-06 01:18), 1.6.1 (2020-01-09 00:02)
Other packages that cited biogram R package
View biogram citation profile
Other R packages that biogram depends, imports, suggests or enhances
Functions, R codes and Examples using the biogram R package
Some associated functions: aaprop . add_1grams . as.data.frame.feature_test . binarize . biogram-package . calc_criterion . calc_cs . calc_ed . calc_ig . calc_kl . calc_pi . calc_si . check_criterion . cluster_reg_exp . code_ngrams . construct_ngrams . count_multigrams . count_ngrams . count_specified . count_total . create_encoding . create_feature_target . create_ngrams . criterion_distribution . cut.feature_test . decode_ngrams . degenerate . degenerate_ngrams . distr_crit . encoding2df . fast_crosstable . feature_test . full2simple . gap_ngrams . generate_sequence . generate_single_region . generate_single_unigram . generate_unigrams . get_ngrams_ind . human_cleave . is_ngram . l2n . list2matrix . n2l . ngrams2df . plot.criterion_distribution . position_ngrams . print.feature_test . read_fasta . regenerate . regional_param . seq2ngrams . simple2full . summary.feature_test . table_ngrams . test_features . validate_encoding . write_encoding . write_fasta . 
Some associated R codes: aaprop.R . add_remove_ngrams.R . biogram.R . calc_ed.R . calc_si.R . chi_square.R . cluster_reg_exp.R . construct_ngrams.R . count_multigrams.R . count_ngrams.R . count_specified.R . create_encoding.R . criterion_distribution.R . criterions.R . data_manipulation.R . degenerate.R . distr_crit.R . feature_test_class.R . generate_sequence.R . human_cleave.R . indices_and_positions.R . information_gain.R . is_ngram.R . kl_divergence.R . ngram_coding.R . ngrams.R . position_ngrams.R . read_fasta.R . regenerate.R . region.R . seq2matrix.R . simplify.R . table_ngrams.R . test_features.R . utilities.R . write_enc.R .  Full biogram package functions and examples
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