Package: hoardeR 0.10

hoardeR: Collect and Retrieve Annotation Data for Various Genomic Data Using Different Webservices

Cross-species identification of novel gene candidates using the NCBI web service is provided. Further, sets of miRNA target genes can be identified by using the targetscan.org API.

Authors:Daniel Fischer [aut, cre], Anu Sironen [aut]

hoardeR_0.10.tar.gz
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hoardeR_0.10.tgz(r-4.4-emscripten)hoardeR_0.10.tgz(r-4.3-emscripten)
hoardeR.pdf |hoardeR.html✨
hoardeR/json (API)

# Install 'hoardeR' in R:

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

Bug tracker:https://github.com/fischuu/hoarder/issues

Datasets:

species - Available species at NCBI

On CRAN:

3.70 score 1 stars 6 scripts 358 downloads 1 mentions 18 exports 81 dependencies

Last updated 10 months agofrom:b463fc906c. Checks:1 OK, 6 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Jan 26 2025
R-4.5-win	NOTE	Jan 26 2025
R-4.5-mac	NOTE	Jan 26 2025
R-4.5-linux	NOTE	Jan 26 2025
R-4.4-win	NOTE	Jan 26 2025
R-4.4-mac	NOTE	Jan 26 2025
R-4.3-win	NOTE	Dec 27 2024

Exports:blastSeq coverageDensity findSpecies getAnnotation getEnsgInfo getFastaFromBed getGeneLocation getGeneSeq getSequenceFromNCBI intersectXMLAnnot plotCoverage plotHit species subDose subGprobs subPhased tableSpecies targetScan

Dependencies:ade4 askpass bamsignals base64enc BH BiocGenerics BiocParallel Biostrings bitops bslib cachem cli codetools cpp11 crayon curl data.table digest evaluate fastmap fontawesome formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges GenomicTools.fileHandler glue highr htmltools httr IRanges jquerylib jsonlite KernSmooth knitr lambda.r lattice lifecycle magrittr MASS Matrix memoise mime nlme openssl pixmap R.methodsS3 R.oo R.utils R6 rappdirs Rcpp RcppArmadillo RCurl Rhtslib rlang rmarkdown Rsamtools S4Vectors sass segmented seqinr snow snpStats sp stringi stringr survival sys tinytex UCSC.utils vctrs xfun XML XVector yaml zlibbioc

An Introduction to hoardeR

Daniel Fischer and Anu Sironen

Rendered fromhoardeR-vignette.Rmdusingknitr::rmarkdownon Jan 26 2025.

Last update: 2019-02-12
Started: 2016-07-05

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Collect and Retrieve Annotation Data for Various Genomic Data Using Different Web Services.	hoardeR-package
Sending Genomic Sequences to NCBI Blast service	blastSeq
Calculation of the coverage density	coverageDensity
Search in the 'species'` Object.	findSpecies
Downloading or Importing of Annotation Data	getAnnotation
Retrieve Gene Information From the NCBI Database.	getEnsgInfo
Get fasta information based on locations in bed-format	getFastaFromBed
Extracting Gene Locations	getGeneLocation
Extracting a gene sequence from NCBI database.	getGeneSeq
Extracts a sequence from the NCBI webpage	getSequenceFromNCBI
Intersect XML object with annotation object	intersectXMLAnnot
Plots a coverage density object	plotCoverage
Visualization of a cross-species hit	plotHit
Print an fa Object	print,fa-method print.fa
Available species at NCBI	species
Rewrite the Dose File from a Beagle Output	subDose
Rewrite the Gprobs File from a Beagle Output	subGprobs
Rewrite the Phased File from a Beagle Output	subPhased
Summarize an fa Object	summary,fa-method summary.fa
Tables the species in xml file	tableSpecies
Retrieving miRNA target information from targetscan.org	targetScan