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bioc
Biostrings:Efficient manipulation of biological strings
Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.
Maintained by Hervé Pagès. Last updated 1 months ago.
sequencematchingalignmentsequencinggeneticsdataimportdatarepresentationinfrastructurebioconductor-packagecore-package
62 stars 17.77 score 8.6k scripts 1.2k dependentsbioc
BSgenome:Software infrastructure for efficient representation of full genomes and their SNPs
Infrastructure shared by all the Biostrings-based genome data packages.
Maintained by Hervé Pagès. Last updated 2 months ago.
geneticsinfrastructuredatarepresentationsequencematchingannotationsnpbioconductor-packagecore-package
9 stars 14.12 score 1.2k scripts 267 dependentsbioc
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.
Maintained by Felix G.M. Ernst. Last updated 5 months ago.
dataimportdatarepresentationinfrastructuresequencingsoftwarebioconductorbiostringsdnadna-modificationsmodified-nucleotidesnucleotidesrnarna-modification-alphabetrna-modificationssequences
1 stars 6.64 score 5 scripts 8 dependentsbioc
RNAmodR: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.
Maintained by Felix G.M. Ernst. Last updated 5 months ago.
softwareinfrastructureworkflowstepvisualizationsequencingalkanilineseqbioconductormodificationsribomethseqrnarnamodr
3 stars 6.39 score 9 scripts 3 dependentsbioc
Structstrings: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.
Maintained by Felix G.M. Ernst. Last updated 5 months ago.
dataimportdatarepresentationinfrastructuresequencingsoftwarealignmentsequencematchingbioconductorrnarna-structural-analysisrna-structuresequencesstructures
5 stars 6.26 score 3 scripts 4 dependents