Package: LncFinder 1.1.5
LncFinder: LncRNA Identification and Analysis Using Heterologous Features
Long non-coding RNAs identification and analysis. Default models are trained with human, mouse and wheat datasets by employing SVM. Features are based on intrinsic composition of sequence, EIIP value (electron-ion interaction pseudopotential), and secondary structure. This package can also extract other classic features and build new classifiers. Reference: Han SY., Liang YC., Li Y., et al. (2018) <doi:10.1093/bib/bby065>.
Authors:
LncFinder_1.1.5.tar.gz
LncFinder_1.1.5.zip(r-4.5)LncFinder_1.1.5.zip(r-4.4)LncFinder_1.1.5.zip(r-4.3)
LncFinder_1.1.5.tgz(r-4.4-any)LncFinder_1.1.5.tgz(r-4.3-any)
LncFinder_1.1.5.tar.gz(r-4.5-noble)LncFinder_1.1.5.tar.gz(r-4.4-noble)
LncFinder_1.1.5.tgz(r-4.4-emscripten)LncFinder_1.1.5.tgz(r-4.3-emscripten)
LncFinder.pdf |LncFinder.html✨
LncFinder/json (API)
NEWS
| # Install 'LncFinder' in R: |
| install.packages('LncFinder', repos = c('https://han-siyu.r-universe.dev', 'https://cloud.r-project.org')) |
- demo_DNA.seq - A demo of DNA sequences
- demo_SS.seq - A demo of secondary structure sequences
- demo_dataset - A demo of dataset
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 3 years agofrom:7130d67719. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Aug 28 2024 |
| R-4.5-win | OK | Aug 28 2024 |
| R-4.5-linux | OK | Aug 28 2024 |
| R-4.4-win | OK | Aug 28 2024 |
| R-4.4-mac | OK | Aug 28 2024 |
| R-4.3-win | OK | Aug 28 2024 |
| R-4.3-mac | OK | Aug 28 2024 |
Exports:build_modelcompute_EIIPcompute_EucDistancecompute_FickettScorecompute_GCcompute_hexamerScorecompute_kmercompute_LogDistancecompute_pIextract_featuresfind_orfslnc_findermake_frequenciesmake_referFreqread_SSrun_RNAfoldsvm_cvsvm_tune
Dependencies:ade4caretclasscliclockcodetoolscolorspacecpp11data.tablediagramdigestdplyre1071fansifarverforeachfuturefuture.applygenericsggplot2globalsgluegowergtablehardhatipredisobanditeratorsKernSmoothlabelinglatticelavalifecyclelistenvlubridatemagrittrMASSMatrixmgcvModelMetricsmunsellnlmennetnumDerivparallellypillarpixmappkgconfigplyrpROCprodlimprogressrproxypurrrR6RColorBrewerRcppRcppArmadillorecipesreshape2rlangrpartscalessegmentedseqinrshapespSQUAREMstringistringrsurvivaltibbletidyrtidyselecttimechangetimeDatetzdbutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Build Users' Own Model | build_model |
| Extract the EIIP-derived features | compute_EIIP |
| Compute Euclidean Distance | compute_EucDistance |
| Compute Fickett TESTCODE Score | compute_FickettScore |
| Calculate GC content | compute_GC |
| Compute Hexamer Score | compute_hexamerScore |
| Compute _k_-mer Features | compute_kmer |
| Compute Logarithm Distance | compute_LogDistance |
| Compute Theoretical Isoelectric Point | compute_pI |
| A demo of dataset | demo_dataset |
| A demo of DNA sequences | demo_DNA.seq |
| A demo of secondary structure sequences | demo_SS.seq |
| Extract the Features | extract_features |
| Find ORFs | find_orfs |
| Long Non-coding RNA Identification | lnc_finder |
| Make the frequencies file for new classifier construction | make_frequencies |
| Make Frequencies File for Log.Dist, Euc.Dist, and hexamer score | make_referFreq |
| Read Secondary Structure Information | read_SS |
| Obtain the Secondary Structure Sequences Using RNAfold | run_RNAfold |
| _k_-fold Cross Validation for SVM | svm_cv |
| Parameter Tuning of SVM | svm_tune |
