codLncScape provides a self-enriching framework for systematic collection and exploration of coding lncRNAs
We are delighted to announce that our paper has been published in Advanced Science. We encourage researchers to utilize and cite our work to further the study of coding lncRNAs. For reference, please use the following link: https://doi.org/10.1002/advs.202400009.
This research was collaboratively conducted by Tianyuan Liu, Huiyuan Qiao, Zixu Wang et al.
codingLncRNA is a utility package available both in R and Python, designed to facilitate easy management and retrieval of lncRNAs which code peptides, including RNA sequences, peptide sequences, and ORF sequences. In addition, this Scripts directory is an integral part of the codLncScape dedicated to the bioinformatics analysis of coding lncRNAs.
To install the codingLncRNA R package, make sure you have the devtools package installed and loaded in your R session. You can install it using:
install.packages("devtools")Then, install codingLncRNA from GitHub with:
devtools::install_github("ShellyCoder/codingLncRNA/R/codingLncRNA")- Creating LncRNAData Object
First, we will utilize the LncRNAData function to create an object of LncRNAData, which incorporates the sample data included in the package.
library(codingLncRNA)
lncRNAData <- LncRNAData()- Retrieving RNA, Peptide, and ORF Sequences
The codingLncRNA package offers several methods that allow the user to access and retrieve RNA, peptide, and ORF sequences:
lncRNAData <- getRNA(lncRNAData)
lncRNAData <- getPeptide(lncRNAData)
lncRNAData <- getORF(lncRNAData)Each method retrieves the corresponding sequences and stores them as a dataframe in the respective slot of the LncRNAData object. For instance, to view the retrieved RNA sequences, you can utilize the following command:
View(lncRNAData@data)
View(lncRNAData@rna)
View(lncRNAData@peptide)
View(lncRNAData@orf)To install the codingLncRNA Python package, you can use pip to install directly from GitHub:
pip install git+https://github.com/ShellyCoder/codingLncRNA.git#subdirectory=python- Loading Data:
from codingLncRNA import LncRNAData, load_data
# Load data
lncRNAData = LncRNAData()- Retrieving Sequences:
# Get RNA sequences
rna_sequences = lncRNAData.getRNA()
# Get Peptide sequences
peptide_sequences = lncRNAData.getPeptide()
# Get ORF sequences
orf_sequences = lncRNAData.getORF()This package is still under development. For any issues or suggestions, please submit an issue on the GitHub repository.