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Package: factR 1.12.0

Fursham Hamid

factR: Functional Annotation of Custom Transcriptomes

factR contain tools to process and interact withcustom-assembled transcriptomes (GTF). At its core, factRconstructs CDS information on custom transcripts andsubsequently predicts its functional output. In addition, factRhas tools capable of plotting transcripts, correctingchromosome and gene information and shortlisting newtranscripts.

Authors:Fursham Hamid [aut, cre]

factR_1.12.0.tar.gz
factR_1.12.0.zip(r-4.6)factR_1.12.0.zip(r-4.5)factR_1.12.0.zip(r-4.4)
factR_1.12.0.tgz(r-4.6-any)factR_1.12.0.tgz(r-4.5-any)
factR_1.12.0.tar.gz(r-4.6-any)factR_1.12.0.tar.gz(r-4.5-any)
factR_1.12.0.tgz(r-4.5-emscripten)
factR.pdf |factR.html✨
factR/json (API)
NEWS

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

Bug tracker:https://github.com/fursham-h/factr/issues

Pkgdown/docs site:https://fursham-h.github.io

Datasets:
  • chrom_matched_query_gtf - Chromosome matched version of "query_gtf"
  • domains.known - Example output of predictDomains
  • domains.out - Example output of predictDomains
  • matched_query_gtf - Seqlevels and gene_id matched query data
  • new_query_gtf - Query data containing CDS information
  • query_cds - CDS from 4 transcripts entries of the same gene
  • query_exons - GRangeList of exons from 4 transcripts entries from query_gtf
  • query_gtf - Imported GTF file containing 4 transcript entries of the same gene
  • ref_cds - CDS from 2 reference transcripts entries of the same gene
  • ref_exons - Exons from 2 reference transcripts entries of the same gene
  • ref_gtf - Imported GTF file containing 2 reference transcript entries of the same gene

On BioConductor:factR-1.13.0(bioc 3.23)factR-1.12.0(bioc 3.22)

alternativesplicingfunctionalpredictiongenepredictioncustom-transcriptomesfunctional-annotationgtfrna-seq-analysis

4.30 score 2 stars 8 scripts 254 downloads 14 exports 102 dependencies

Last updated from:1edd734419 (on RELEASE_3_22). Checks:1 NOTE, 9 OK. Indexed: no.

TargetResultTotal timeArtifact
bioc-checksNOTE203
linux-devel-x86_64OK353
source / vignettesOK477
linux-release-x86_64OK340
macos-devel-arm64OK311
macos-release-arm64OK255
windows-develOK246
windows-releaseOK225
windows-oldrelOK305
wasm-releaseOK214

Exports:buildCDSfiltereachhas_consistentSeqlevelsimportFASTAimportGTFmatchChromosomesmatchGeneInfomutateeachpredictDomainspredictNMDsorteachsubsetNewTranscriptstrimTranscriptsviewTranscripts

Dependencies:abindAnnotationDbiaskpassassertthatBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobcachemcigarilloclicliprcodetoolscowplotcpp11crayoncurldata.tableDBIDelayedArraydplyrdrawProteinsfarverfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegtablehmshttrIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpbapplypillarpkgconfigplogrpngprettyunitsprogresspurrrR6RColorBrewerRCurlreadrrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsviridisLitevroomwiggleplotrwithrXMLXVectoryaml

Using factR

Fursham Hamid

Rendered fromfactR.Rmdusingknitr::rmarkdownon Jan 23 2026.

Last update: 2022-07-04
Started: 2019-12-27

Citation

Development and contributors

Readme and manuals

Help Manual

Help pageTopics
Reference-guided construction of CDS on GTF objectbuildCDS
Chromosome matched version of "query_gtf"chrom_matched_query_gtf
Example output of predictDomains()domains.known
Example output of predictDomains()domains.out
Internally filter each element of a GenomicRangesListfiltereach
Test consistency of chromosome naming styles (aka seqlevels; e.g. "chr1" vs "1") across multiple objectshas_consistentSeqlevels
Import FASTA file into RimportFASTA
Import GTF file into RimportGTF
Match seqlevels of input GRanges to reference GRanges or BioString objectsmatchChromosomes
Seqlevels and gene_id matched query datamatched_query_gtf
Match gene metadata from query GTF to a reference GTFmatchGeneInfo
Internally create or transform metadata of a GenomicRangesListmutateeach
Query data containing CDS informationnew_query_gtf
Predict protein domain families from coding transcriptspredictDomains
Predict NMD sensitivity on mRNA transcriptspredictNMD
CDS from 4 transcripts entries of the same genequery_cds
GRangeList of exons from 4 transcripts entries from query_gtfquery_exons
Imported GTF file containing 4 transcript entries of the same genequery_gtf
CDS from 2 reference transcripts entries of the same generef_cds
Exons from 2 reference transcripts entries of the same generef_exons
Imported GTF file containing 2 reference transcript entries of the same generef_gtf
Internally sort each element of a GenomicRangesListsorteach
Shortlist GTF GRanges object for new transcriptssubsetNewTranscripts
Resize 5' and 3' ends of a transcript GenomicRangestrimTranscripts
Plot transcripts directly from GTF.viewTranscripts

Usage by other packages (reverse dependencies)

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