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bioc
tRNA:Analyzing tRNA sequences and structures
The tRNA package allows tRNA sequences and structures to be accessed and used for subsetting. In addition, it provides visualization tools to compare feature parameters of multiple tRNA sets and correlate them to additional data. The tRNA package uses GRanges objects as inputs requiring only few additional column data sets.
Maintained by Felix GM Ernst. Last updated 5 months ago.
softwarevisualizationbioconductorsequencesstructurestrna
98.3 match 1 stars 6.81 score 3 scripts 3 dependentsbioc
tRNAdbImport:Importing from tRNAdb and mitotRNAdb as GRanges objects
tRNAdbImport imports the entries of the tRNAdb and mtRNAdb (http://trna.bioinf.uni-leipzig.de) as GRanges object.
Maintained by Felix G.M. Ernst. Last updated 5 months ago.
softwarevisualizationdataimportbioconductorsequencesstructurestrnatrna-genestrna-sequencestrnadb
30.1 match 1 stars 5.26 score 3 scripts 1 dependentsbioc
tRNAscanImport:Importing a tRNAscan-SE result file as GRanges object
The package imports the result of tRNAscan-SE as a GRanges object.
Maintained by Felix G.M. Ernst. Last updated 5 months ago.
softwaredataimportworkflowsteppreprocessingvisualizationbioconductorsequencesstructurestrnatrnascantrnascan-se
14.1 match 2 stars 5.08 score 3 scripts
mt1022
cubar:Codon Usage Bias Analysis
A suite of functions for rapid and flexible analysis of codon usage bias. It provides in-depth analysis at the codon level, including relative synonymous codon usage (RSCU), tRNA weight calculations, machine learning predictions for optimal or preferred codons, and visualization of codon-anticodon pairing. Additionally, it can calculate various gene- specific codon indices such as codon adaptation index (CAI), effective number of codons (ENC), fraction of optimal codons (Fop), tRNA adaptation index (tAI), mean codon stabilization coefficients (CSCg), and GC contents (GC/GC3s/GC4d). It also supports both standard and non-standard genetic code tables found in NCBI, as well as custom genetic code tables.
Maintained by Hong Zhang. Last updated 3 months ago.
bioinformaticscodon-usagemachine-learningsequence-analysis
11.4 match 6 stars 5.82 score 8 scriptsbioc
GenomicFeatures:Query the gene models of a given organism/assembly
Extract the genomic locations of genes, transcripts, exons, introns, and CDS, for the gene models stored in a TxDb object. A TxDb object is a small database that contains the gene models of a given organism/assembly. Bioconductor provides a small collection of TxDb objects in the form of ready-to-install TxDb packages for the most commonly studied organisms. Additionally, the user can easily make a TxDb object (or package) for the organism/assembly of their choice by using the tools from the txdbmaker package.
Maintained by H. Pagès. Last updated 4 months ago.
geneticsinfrastructureannotationsequencinggenomeannotationbioconductor-packagecore-package
1.8 match 26 stars 15.34 score 5.3k scripts 339 dependents
cran
MINTplates:Encode "License-Plates" from Sequences and Decode Them Back
It can be used to create/encode molecular "license-plates" from sequences and to also decode the "license-plates" back to sequences. While initially created for transfer RNA-derived small fragments (tRFs), this tool can be used for any genomic sequences including but not limited to: tRFs, microRNAs, etc. The detailed information can reference to Pliatsika V, Loher P, Telonis AG, Rigoutsos I (2016) <doi:10.1093/bioinformatics/btw194>. It can also be used to annotate tRFs. The detailed information can reference to Loher P, Telonis AG, Rigoutsos I (2017) <doi:10.1038/srep41184>.
Maintained by Shanliang Zhong. Last updated 4 years ago.
5.5 match 1.00 score