Package: mobileRNA 1.3.0

Katie Jeynes-Cupper

mobileRNA: mobileRNA: Investigate the RNA mobilome & population-scale changes

Genomic analysis can be utilised to identify differences between RNA populations in two conditions, both in production and abundance. This includes the identification of RNAs produced by multiple genomes within a biological system. For example, RNA produced by pathogens within a host or mobile RNAs in plant graft systems. The mobileRNA package provides methods to pre-process, analyse and visualise the sRNA and mRNA populations based on the premise of mapping reads to all genotypes at the same time.

Authors:Katie Jeynes-Cupper [aut, cre], Marco Catoni [aut]

mobileRNA_1.3.0.tar.gz
mobileRNA_1.3.0.zip(r-4.5)mobileRNA_1.3.0.zip(r-4.4)mobileRNA_1.3.0.zip(r-4.3)
mobileRNA_1.3.0.tgz(r-4.4-any)mobileRNA_1.3.0.tgz(r-4.3-any)
mobileRNA_1.3.0.tar.gz(r-4.5-noble)mobileRNA_1.3.0.tar.gz(r-4.4-noble)
mobileRNA_1.3.0.tgz(r-4.4-emscripten)mobileRNA_1.3.0.tgz(r-4.3-emscripten)
mobileRNA.pdf |mobileRNA.html✨
mobileRNA/json (API)
NEWS

# Install 'mobileRNA' in R:
install.packages('mobileRNA', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/kjeynescupper/mobilerna/issues

Datasets:
  • mRNA_data - MRNA_data: simulated messenger RNA data for biological replicates
  • sRNA_data - SRNA_data: simulated data for biological replicates

On BioConductor:mobileRNA-1.3.0(bioc 3.21)mobileRNA-1.2.0(bioc 3.20)

visualizationrnaseqsequencingsmallrnagenomeassemblyclusteringexperimentaldesignqualitycontrolworkflowstepalignmentpreprocessingbioinformaticsplant-science

5.45 score 4 stars 2 scripts 140 downloads 20 exports 138 dependencies

Last updated 2 months agofrom:d0f0d6ca3e. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 29 2024
R-4.5-winOKNov 29 2024
R-4.5-linuxOKNov 29 2024
R-4.4-winOKNov 29 2024
R-4.4-macOKNov 29 2024
R-4.3-winOKNov 29 2024
R-4.3-macOKNov 29 2024

Exports:mapRNAplotHeatmapplotRNAfeaturesplotSampleDistanceplotSamplePCARNAattributesRNAdf2seRNAdicercallRNAdifferentialAnalysisRNAdistributionRNAfeaturesRNAimportRNAmergeAnnotationsRNAmergeGenomesRNAmobileRNApopulationRNAreorderRNAsequencesRNAsubsetRNAsummary

Dependencies:abindapeaskpassaudiobeeprBHBiobaseBiocGenericsBiocIOBiocParallelbioseqBiostringsbitbit64bitopsbriocallrclicliprcodetoolscolorspacecpp11crayoncurldata.tableDelayedArraydescDESeq2diffobjdigestdplyredgeRevaluatefansifarverformatRfsfutile.loggerfutile.optionsfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2ggrepelglobalsgluegtableherehmshttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclelimmalistenvlocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslparallellypbapplypheatmappillarpkgbuildpkgconfigpkgloadpngpraiseprettyunitsprocessxprogressprogressrpspurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppArmadilloRcppTOMLRCurlreadrrestfulrreticulateRhtslibrjsonrlangrprojrootRPushbulletRsamtoolsrtracklayerS4ArraysS4VectorsscalessessioninfoSimDesignsnowSparseArraystatmodstringdiststringistringrSummarizedExperimentsystestthattibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsviridisLitevroomwaldowithrXMLXVectoryamlzlibbioc

mobileRNA: Investigate the RNA mobilome & population-scale changes.

Katie Jeynes-Cupper, Marco Catoni

Rendered frommobileRNA.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2024-05-08
Started: 2023-06-05

Readme and manuals

Help Manual

Help pageTopics
mobileRNA pre-processing method for sRNAseq & mRNAseq (alignment, raw count or cluster analysis)mapRNA
mRNA_data: simulated messenger RNA data for biological replicatesmRNA_data
Heatmap of log-transformed normalization dataplotHeatmap
Plots the distribution of genomic features in the genome and those that overlap with sRNA clustersplotRNAfeatures
Sample distance matrixplotSampleDistance
PCA plot of PC1 and PC2plotSamplePCA
Overlap the genomic features related to the sRNA clustersRNAattributes
Convert a 'mobileRNA' dataframe to a SummarizedExperiment objectRNAdf2se
Define the consensus dicercall for each sRNA clusterRNAdicercall
Differential Analysis using 'DESeq2' or 'edgeR'RNAdifferentialAnalysis
Plot the distribution of sRNA classes based on nucleotide lengthRNAdistribution
Summarise the distribution of sRNA clusters across genomic featuresRNAfeatures
Import and organise sRNAseq & mRNAseq data setsRNAimport
Merge two genome annotation files (GFF Format)RNAmergeAnnotations
Merge two genome reference assemblies (FASTA format)RNAmergeGenomes
Identify putative RNA molecules produced by the non-tissue sample genomeRNAmobile
Identify gained/lost RNA populations between treatment and control conditionsRNApopulation
Reorder the data frame for differential analysis, ensuring control verse treatment comparisonRNAreorder
Extract RNA sequence from sRNA clustersRNAsequences
Subset sRNA data based on dicercall sizeRNAsubset
Summarise differential analysis resultsRNAsummary
sRNA_data: simulated data for biological replicatessRNA_data