Package: factR 1.14.0

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_1.14.0.tar.gz
factR_1.14.0.zip(r-4.7-any)factR_1.14.0.zip(r-4.6-any)factR_1.14.0.zip(r-4.5-any)
factR_1.14.0.tgz(r-4.6-any)factR_1.14.0.tgz(r-4.5-any)
factR_1.14.0.tar.gz(r-4.7-any)factR_1.14.0.tar.gz(r-4.6-any)
factR_1.14.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
factR/json (API)

# 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-1.15.0(bioc 3.24)factR-1.14.0(bioc 3.23)

alternativesplicing functionalprediction geneprediction custom-transcriptomes functional-annotation gtf rna-seq-analysis

4.38 score 2 stars 12 scripts 368 downloads 14 exports 101 dependencies

Last updated from:245db19a73 (on RELEASE_3_23). Checks:1 NOTE, 2 ERROR, 7 OK. Indexed: no.

Target	Result	Time
bioc-checks	NOTE	231
linux-devel	ERROR	371
source / vignettes	OK	394
linux-release	OK	346
macos-release	OK	268
macos-oldrel	OK	206
windows-devel	ERROR	238
windows-release	OK	222
windows-oldrel	OK	254
wasm-release	OK	223

Exports:buildCDS filtereach has_consistentSeqlevels importFASTA importGTF matchChromosomes matchGeneInfo mutateeach predictDomains predictNMD sorteach subsetNewTranscripts trimTranscripts viewTranscripts

Dependencies:abind AnnotationDbi askpass assertthat BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob cachem cigarillo cli clipr codetools cowplot cpp11 crayon curl data.table DBI DelayedArray dplyr drawProteins farver fastmap formatR futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gtable hms httr IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pbapply pillar pkgconfig png prettyunits progress purrr R6 RColorBrewer RCurl readr restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors S7 scales Seqinfo snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tzdb UCSC.utils utf8 vctrs viridisLite vroom wiggleplotr withr XML XVector yaml

Using factR

Rendered fromfactR.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Reference-guided construction of CDS on GTF object	buildCDS
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 GenomicRangesList	filtereach
Test consistency of chromosome naming styles (aka seqlevels; e.g. "chr1" vs "1") across multiple objects	has_consistentSeqlevels
Import FASTA file into R	importFASTA
Import GTF file into R	importGTF
Match seqlevels of input GRanges to reference GRanges or BioString objects	matchChromosomes
Seqlevels and gene_id matched query data	matched_query_gtf
Match gene metadata from query GTF to a reference GTF	matchGeneInfo
Internally create or transform metadata of a GenomicRangesList	mutateeach
Query data containing CDS information	new_query_gtf
Predict protein domain families from coding transcripts	predictDomains
Predict NMD sensitivity on mRNA transcripts	predictNMD
CDS from 4 transcripts entries of the same gene	query_cds
GRangeList of exons from 4 transcripts entries from query_gtf	query_exons
Imported GTF file containing 4 transcript entries of the same gene	query_gtf
CDS from 2 reference transcripts entries of the same gene	ref_cds
Exons from 2 reference transcripts entries of the same gene	ref_exons
Imported GTF file containing 2 reference transcript entries of the same gene	ref_gtf
Internally sort each element of a GenomicRangesList	sorteach
Shortlist GTF GRanges object for new transcripts	subsetNewTranscripts
Resize 5' and 3' ends of a transcript GenomicRanges	trimTranscripts
Plot transcripts directly from GTF.	viewTranscripts