fischuu / hoarder

R-package for information retrieval from NCBI databases, with main focus on Blast.

hoardeR

R-package for information retrieval from various bioinformatic-related databases.

Installation

The package depends on quite a few libraries and it can be cumbersome to install them manually. The easiest way to install the latest version of the package is with the help of the devtools package like this

install.packages("devtools")
devtools::install_github("fischuu/hoardeR")

hoarder's Issues

Export in getFastaFromBed missing

The export function in the getFastaFromBed is still missing

problem with installation

Hi,

Im trying to install hoardeR as i would like to use subPhased, but complains that is not available (for R version 3.4), i have tried with 3.2.5 but get the same problem.
Would you be so kind to help me with this issue?

Thanks a lot,
Laura

Average runtime of blastSeq

Average runtime should only take the finished runs into consideration

continuing a crashed blastSeq run doesn't work

Unable to Use targetScan function with mapply

Hi @fischuu,
I have been using hoardeR for a project and it appears that there is an issue when using it with mapply. Instead of returning the data frame as expected it returns the following. I am providing my test code and will be happy to provide more information. Thanks for all your hard work on this package.
`test <- mapply(targetScan, mirna=c("hsa-miR-99b-5p", "hsa-miR-99b-3p", "hsa-miR-99a-5p"), species = c("Human", "Human", "Human"), release =c("7.2", "7.2", "7.2"), maxOut = c(5,5,5))'

Optimize getFastaFromBed

Currently the function loops through all entries in a bed data frame and loads one fasta file after another. This could be optimized by looping through the required Chromosomes instead, then each chromosomal fasta file would only be loaded once.