Package: factR 1.9.0

Fursham Hamid

factR: Functional Annotation of Custom Transcriptomes

factR contain tools to process and interact with custom-assembled transcriptomes (GTF). At its core, factR constructs CDS information on custom transcripts and subsequently predicts its functional output. In addition, factR has tools capable of plotting transcripts, correcting chromosome and gene information and shortlisting new transcripts.

Authors:Fursham Hamid [aut, cre]

factR_1.9.0.tar.gz
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factR.pdf |factR.html✨
factR/json (API)
NEWS

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

Peer review:

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

Pkgdown: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-1.9.0(bioc 3.21)factR-1.8.0(bioc 3.20)

alternativesplicingfunctionalpredictiongenepredictioncustom-transcriptomesfunctional-annotationgtfrna-seq-analysis

4.00 score 1 stars 5 scripts 132 downloads 14 exports 107 dependencies

Last updated 2 months agofrom:c6ff9f0a24. 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:buildCDSfiltereachhas_consistentSeqlevelsimportFASTAimportGTFmatchChromosomesmatchGeneInfomutateeachpredictDomainspredictNMDsorteachsubsetNewTranscriptstrimTranscriptsviewTranscripts

Dependencies:abindAnnotationDbiaskpassassertthatBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobcachemclicliprcodetoolscolorspacecowplotcpp11crayoncurldata.tableDBIDelayedArraydplyrdrawProteinsfansifarverfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegtablehmshttrIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpbapplypillarpkgconfigplogrpngprettyunitsprogresspurrrR6RColorBrewerRCurlreadrrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscalessnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsviridisLitevroomwiggleplotrwithrXMLXVectoryamlzlibbioc

Using factR

Fursham Hamid

Rendered fromfactR.Rmdusingknitr::rmarkdownon Nov 29 2024.

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

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