Package: packFinder 1.19.0

Jack Gisby

packFinder: de novo Annotation of Pack-TYPE Transposable Elements

Algorithm and tools for in silico pack-TYPE transposon discovery. Filters a given genome for properties unique to DNA transposons and provides tools for the investigation of returned matches. Sequences are input in DNAString format, and ranges are returned as a dataframe (in the format returned by as.dataframe(GRanges)).

Authors:Jack Gisby [aut, cre], Marco Catoni [aut]

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packFinder.pdf |packFinder.html✨
packFinder/json (API)
NEWS

# Install 'packFinder' in R:

install.packages('packFinder', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/jackgisby/packfinder/issues

Datasets:

arabidopsisThalianaRefseq - Arabidopsis thaliana Refseq Genome Chromosome 3 Subset
packMatches - Sample packFinder Output

On BioConductor:packFinder-1.19.0(bioc 3.21)packFinder-1.18.0(bioc 3.20)

genetics sequencematching annotation bioinformatics text-mining

4.78 score 6 stars 6 scripts 190 downloads 22 exports 27 dependencies

Last updated 2 months agofrom:7ce40932f6. Checks:OK: 3 NOTE: 4. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 05 2024
R-4.5-win	NOTE	Dec 05 2024
R-4.5-linux	NOTE	Dec 05 2024
R-4.4-win	NOTE	Dec 05 2024
R-4.4-mac	NOTE	Dec 05 2024
R-4.3-win	OK	Dec 05 2024
R-4.3-mac	OK	Dec 05 2024

Exports:blastAnalysis blastAnnotate collapseSeqs filterWildcards getPackSeqs getPacksFromCsv getPacksFromFasta getPacksFromGRanges getTsds identifyPotentialPackElements identifyTirMatches makeBlastDb packAlign packBlast packClust packSearch packsToCsv packsToFasta packsToGRanges readBlast readUc tirClust

Dependencies:ape askpass BiocGenerics Biostrings crayon curl digest generics GenomeInfoDb GenomeInfoDbData GenomicRanges httr IRanges jsonlite kmer lattice mime nlme openssl phylogram R6 Rcpp S4Vectors sys UCSC.utils XVector zlibbioc

packFinder

Jack Gisby

Rendered frompackFinder.Rmdusingknitr::rmarkdownon Dec 05 2024.

Last update: 2022-07-18
Started: 2019-10-13

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Arabidopsis thaliana Refseq Genome Chromosome 3 Subset	arabidopsisThalianaRefseq
BLAST Analysis of PackTYPE Elements	blastAnalysis
Functional Annotation of PackTYPE Elements	blastAnnotate
Collapse Overlapping Sequences	collapseSeqs
Remove Low Quality Sequences	filterWildcards
Extract Sequences of Pack-TYPE Elements	getPackSeqs
Retrieve Saved packFinder Results (.csv)	getPacksFromCsv
Retrieve Saved packFinder Results (.fasta)	getPacksFromFasta
Retrieve packFinder Results from GRanges Object	getPacksFromGRanges
Get Flanking Terminal Site Duplication Sequences	getTsds
Pack Element Filtering	identifyPotentialPackElements
Identify Terminal Inverted Repeat Matches	identifyTirMatches
Make Blast Database	makeBlastDb
Global Alignment with VSEARCH	packAlign
Pipeline for BLAST/Classification of PackTYPE Elements	packBlast
Cluster Transposons with VSEARCH	packClust
packFinder: a package for the de novo Annotation of Pack-TYPE Transposable Elements	packFinder
Sample packFinder Output	packMatches
packFinder Algorithm Pipeline	packSearch
Save packFinder Results in CSV Format (.csv)	packsToCsv
Save packFinder Results in FASTA Format (.fasta)	packsToFasta
Export packFinder Results to a GRanges Object	packsToGRanges
Convert NCBI BLAST+ Files to Dataframe	readBlast
Convert .uc Files to Dataframe	readUc
Analyse TIR Sequences of Pre-clustered Transposable Elements	tirClust