ROCR - Visualizing the Performance of Scoring Classifiers

ROC graphs, sensitivity/specificity curves, lift charts, and precision/recall plots are popular examples of trade-off visualizations for specific pairs of performance measures. ROCR is a flexible tool for creating cutoff-parameterized 2D performance curves by freely combining two from over 25 performance measures (new performance measures can be added using a standard interface). Curves from different cross-validation or bootstrapping runs can be averaged by different methods, and standard deviations, standard errors or box plots can be used to visualize the variability across the runs. The parameterization can be visualized by printing cutoff values at the corresponding curve positions, or by coloring the curve according to cutoff. All components of a performance plot can be quickly adjusted using a flexible parameter dispatching mechanism. Despite its flexibility, ROCR is easy to use, with only three commands and reasonable default values for all optional parameters.

Last updated 6 months ago

38 stars 9.00 score 5 dependencies 202 dependents

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.

Last updated 4 months ago

softwarevisualization

2.76 score 50 dependencies 3 dependents

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.

Last updated 4 months ago

dataimportdatarepresentationinfrastructuresequencingsoftware

2.22 score 27 dependencies 8 dependents

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.

Last updated 4 months ago

dataimportdatarepresentationinfrastructuresequencingsoftwarealignmentsequencematching

4 stars 1.85 score 26 dependencies 4 dependents

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.

Last updated 4 months ago

softwareinfrastructureworkflowstepvisualizationsequencing

3 stars 1.64 score 157 dependencies 3 dependents

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.

Last updated 4 months ago

softwarevisualizationdataimportbioconductorsequencesstructurestrnatrna-genestrna-sequencestrnadb

1 stars 1.24 score 54 dependencies 1 dependents

tRNAscanImport - Importing a tRNAscan-SE result file as GRanges object

The package imports the result of tRNAscan-SE as a GRanges object.

Last updated 4 months ago

softwaredataimportworkflowsteppreprocessingvisualization

2 stars 1.00 score 80 dependencies

EpiTxDb - 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.

Last updated 4 months ago

softwareepitranscriptomics

0.82 score 112 dependencies

RNAmodR.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.

Last updated 4 months ago

softwareinfrastructureworkflowstepvisualizationsequencing

0.61 score 159 dependencies

RNAmodR.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.

Last updated 4 months ago

softwareworkflowstepvisualizationsequencing

2 stars 0.61 score 158 dependencies

RNAmodR.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.

Last updated 4 months ago

softwareworkflowstepvisualizationsequencing

1 stars 0.49 score 158 dependencies