bioc-issue-bot
commented
7 years ago Hi @matdoering
Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.
The DESCRIPTION file for this package is:
Package: openPrimeR
Title: Multiplex PCR Primer Design and Analysis
Version: 0.99.0
Authors@R: c(person("Matthias", "Döring",
email = "mdoering@mpi-inf.mpg.de",
role = c("aut", "cre")),
person("Nico", "Pfeifer",
email = "pfeifer@informatik.uni-tuebingen.de",
role = c("aut"))
)
Description: An implementation of methods for designing, evaluating,
and comparing primer sets for multiplex PCR.
Primers are designed by solving a set cover problem such that
the number of covered template sequences is maximized with
the smallest possible set of primers.
To guarantee that high-quality primers are generated,
only primers fulfilling constraints on their physicochemical properties
are selected. All relevant functions are accessible through
a user-friendly Shiny application.
Depends:
R (>= 3.4.0)
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Imports:
Biostrings (>= 2.38.4),
XML (>= 3.98-1.4),
scales (>= 0.4.0),
reshape2 (>= 1.4.1),
seqinr (>= 3.3-3),
IRanges (>= 2.4.8),
GenomicRanges (>= 1.22.4),
ggplot2 (>= 2.1.0),
plyr (>= 1.8.4),
dplyr (>= 0.5.0),
stringdist (>= 0.9.4.1),
stringr (>= 1.0.0),
RColorBrewer (>= 1.1-2),
DECIPHER (>= 1.16.1),
lpSolveAPI (>= 5.5.2.0-17),
digest (>= 0.6.9),
Hmisc (>= 3.17-4),
ape (>= 3.5),
BiocGenerics (>= 0.16.1),
S4Vectors (>= 0.8.11),
foreach (>= 1.4.3),
magrittr (>= 1.5),
distr (>= 2.6),
distrEx (>= 2.6),
fitdistrplus (>= 1.0-7),
uniqtag (>= 1.0),
openxlsx (>= 4.0.17),
grid (>= 3.1.0),
grDevices (>= 3.1.0),
stats (>= 3.1.0),
utils (>= 3.1.0),
methods (>= 3.1.0)
Suggests:
shiny (>= 1.0.2),
shinyjs (>= 0.9),
shinyBS (>= 0.61),
DT (>= 0.2),
testthat (>= 1.0.2),
knitr (>= 1.13),
rmarkdown (>= 1.0),
devtools (>= 1.12.0),
doParallel (>= 1.0.10),
pander (>= 0.6.0),
learnr (>= 0.9)
SystemRequirements: MAFFT (>= 7.305),
OligoArrayAux (>= 3.8),
ViennaRNA (>= 2.2.4),
MELTING (>= 5.1.1),
Pandoc (>= 1.12.3)
biocViews: Software, Technology
VignetteBuilder: knitr
Collate:
'Comparison.R'
'templates.R'
'primers.R'
'IO.R'
'IO_view.R'
'Ippolito.R'
'RefCoverage.R'
'Tiller.R'
'ambiguity.R'
'check_stop_codons.R'
'con_annealing_temperature.R'
'con_dimerization.R'
'con_gc_clamp.R'
'con_gc_ratio.R'
'con_melting_temperature.R'
'con_primer_coverage.R'
'con_primer_efficiency.R'
'con_primer_secondary_structures.R'
'con_repeats.R'
'con_runs.R'
'con_template_secondary_structures.R'
'constraints.R'
'constraints_eval.R'
'errors.R'
'filters.R'
'helper_functions.R'
'initialize_primers.R'
'initialize_primers_tree.R'
'openPrimeR.R'
'optimization_ILP.R'
'optimization_algo.R'
'optimization_global.R'
'optimization_greedy.R'
'plots_comparison.R'
'settings.R'
'plots_constraints.R'
'plots_coverage.R'
'plots_filtering.R'
'primer_significance.R'
'startApp.R'
'zzz.R'
lawremi
matdoering
vobencha
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