Modstrings - Working with modified nucleotide sequences
Representing nucleotide modifications in a nucleotide sequence is usually done via special characters from a number of sources. This represents a challenge to work with in R and the Biostrings package. The Modstrings package implements this functionallity for RNA and DNA sequences containing modified nucleotides by translating the character internally in order to work with the infrastructure of the Biostrings package. For this the ModRNAString and ModDNAString classes and derivates and functions to construct and modify these objects despite the encoding issues are implemenented. In addition the conversion from sequences to list like location information (and the reverse operation) is implemented as well.
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dataimportdatarepresentationinfrastructuresequencingsoftwarebioconductorbiostringsdnadna-modificationsmodified-nucleotidesnucleotidesrnarna-modification-alphabetrna-modificationssequences
7.08 score 2 stars 9 dependents 9 scripts 506 downloadstRNA - 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.
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softwarevisualizationbioconductorsequencesstructurestrna
6.64 score 1 stars 4 dependents 10 scripts 565 downloadsRNAmodR - Detection of post-transcriptional modifications in high throughput sequencing data
RNAmodR provides classes and workflows for loading/aggregation data from high througput sequencing aimed at detecting post-transcriptional modifications through analysis of specific patterns. In addition, utilities are provided to validate and visualize the results. The RNAmodR package provides a core functionality from which specific analysis strategies can be easily implemented as a seperate package.
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softwareinfrastructureworkflowstepvisualizationsequencingalkanilineseqbioconductormodificationsribomethseqrnarnamodr
6.53 score 3 stars 3 dependents 14 scripts 584 downloadsStructstrings - Implementation of the dot bracket annotations with Biostrings
The Structstrings package implements the widely used dot bracket annotation for storing base pairing information in structured RNA. Structstrings uses the infrastructure provided by the Biostrings package and derives the DotBracketString and related classes from the BString class. From these, base pair tables can be produced for in depth analysis. In addition, the loop indices of the base pairs can be retrieved as well. For better efficiency, information conversion is implemented in C, inspired to a large extend by the ViennaRNA package.
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dataimportdatarepresentationinfrastructuresequencingsoftwarealignmentsequencematchingbioconductorrnarna-structural-analysisrna-structuresequencesstructures
6.35 score 5 stars 5 dependents 532 downloadstRNAscanImport - Importing a tRNAscan-SE result file as GRanges object
The package imports the result of tRNAscan-SE as a GRanges object.
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softwaredataimportworkflowsteppreprocessingvisualizationbioconductorsequencesstructurestrnatrnascantrnascan-se
5.38 score 2 stars 1 dependents 558 downloadsRNAmodR.Data - Example data for the RNAmodR package
RNAmodR.Data contains example data, which is used for vignettes and example workflows in the RNAmodR and dependent packages.
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experimentdatasequencingdatarnaseqdatadatapkg
4.97 score 31 scriptstRNAdbImport - 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.
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softwarevisualizationdataimportbioconductorsequencesstructurestrnatrna-genestrna-sequencestrnadb
4.95 score 1 stars 1 dependents 4 scripts 487 downloadsEpiTxDb - Storing and accessing epitranscriptomic information using the AnnotationDbi interface
EpiTxDb facilitates the storage of epitranscriptomic information. More specifically, it can keep track of modification identity, position, the enzyme for introducing it on the RNA, a specifier which determines the position on the RNA to be modified and the literature references each modification is associated with.
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softwareepitranscriptomics
4.82 score 11 scripts 465 downloadsRNAmodR.AlkAnilineSeq - Detection of m7G, m3C and D modification by AlkAnilineSeq
RNAmodR.AlkAnilineSeq implements the detection of m7G, m3C and D modifications on RNA from experimental data generated with the AlkAnilineSeq protocol. The package builds on the core functionality of the RNAmodR package to detect specific patterns of the modifications in high throughput sequencing data.
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softwareworkflowstepvisualizationsequencingalkanilineseqbioconductormodificationsrnarnamodr
4.60 score 2 stars 4 scripts 474 downloadsRNAmodR.RiboMethSeq - Detection of 2'-O methylations by RiboMethSeq
RNAmodR.RiboMethSeq implements the detection of 2'-O methylations on RNA from experimental data generated with the RiboMethSeq protocol. The package builds on the core functionality of the RNAmodR package to detect specific patterns of the modifications in high throughput sequencing data.
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softwareworkflowstepvisualizationsequencingbioconductormodificationsribomethseqrnarnamodr
4.30 score 1 stars 9 scripts 440 downloadsRNAmodR.ML - Detecting patterns of post-transcriptional modifications using machine learning
RNAmodR.ML extend the functionality of the RNAmodR package and classical detection strategies towards detection through machine learning models. RNAmodR.ML provides classes, functions and an example workflow to establish a detection stratedy, which can be packaged.
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softwareinfrastructureworkflowstepvisualizationsequencing
4.00 score 1 stars 3 scripts 519 downloads