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LncFinder

Long Non-Coding RNA Identification and Analysis Utilizing Sequence Intrinsic Composition, Structural Information and Physicochemical Property

Our R Package:

https://CRAN.R-project.org/package=LncFinder
https://github.com/HAN-Siyu/LncFinder/

Our Web Server:

https://bmbl.bmi.osumc.edu/lncfinder/

Reference:

LncFinder: an integrated package for long non-coding RNA identification utilizing sequence intrinsic composition, structural information and physicochemical property, Briefings in Bioinformatics, 2019, 20(6):2009-2027. (doi: "https://doi.org/10.1093/bib/bby065")

The authors would be glad to hear how LncFinder is employed. You are kindly encouraged to notify Siyu HAN <siyu.han@tum.de> about any work you publish.

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Version

Install

install.packages('LncFinder')

Monthly Downloads

238

Version

1.1.6

License

GPL-3

Maintainer

Siyu Han

Last Published

September 28th, 2024

Functions in LncFinder (1.1.6)

read_SS

Read Secondary Structure Information
demo_dataset

A demo of dataset
demo_SS.seq

A demo of secondary structure sequences
lnc_finder

Long Non-coding RNA Identification
svm_cv

k-fold Cross Validation for SVM
run_RNAfold

Obtain the Secondary Structure Sequences Using RNAfold
extract_features

Extract the Features
make_referFreq

Make Frequencies File for Log.Dist, Euc.Dist, and hexamer score
make_frequencies

Make the frequencies file for new classifier construction
svm_tune

Parameter Tuning of SVM
find_orfs

Find ORFs
compute_EucDistance

Compute Euclidean Distance
compute_pI

Compute Theoretical Isoelectric Point
demo_DNA.seq

A demo of DNA sequences
compute_FickettScore

Compute Fickett TESTCODE Score
compute_hexamerScore

Compute Hexamer Score
compute_LogDistance

Compute Logarithm Distance
compute_GC

Calculate GC content
build_model

Build Users' Own Model
compute_EIIP

Extract the EIIP-derived features
compute_kmer

Compute k-mer Features