Showing 7 of total 7 results (show query)
ropensci
restez:Create and Query a Local Copy of 'GenBank' in R
Download large sections of 'GenBank' <https://www.ncbi.nlm.nih.gov/genbank/> and generate a local SQL-based database. A user can then query this database using 'restez' functions or through 'rentrez' <https://CRAN.R-project.org/package=rentrez> wrappers.
Maintained by Joel H. Nitta. Last updated 23 days ago.
26 stars 7.01 score 175 scripts 1 dependents
statgenlmu
coala:A Framework for Coalescent Simulation
Coalescent simulators can rapidly simulate biological sequences evolving according to a given model of evolution. You can use this package to specify such models, to conduct the simulations and to calculate additional statistics from the results (Staab, Metzler, 2016 <doi:10.1093/bioinformatics/btw098>). It relies on existing simulators for doing the simulation, and currently supports the programs 'ms', 'msms' and 'scrm'. It also supports finite-sites mutation models by combining the simulators with the program 'seq-gen'. Coala provides functions for calculating certain summary statistics, which can also be applied to actual biological data. One possibility to import data is through the 'PopGenome' package (<https://github.com/pievos101/PopGenome>).
Maintained by Dirk Metzler. Last updated 1 years ago.
coalescentdnaevolutionpopgensimulationcpp
23 stars 6.76 score 84 scripts
bioc
Modstrings:Working with modified nucleotide sequences
Representing nucleotide modifications in a nucleotide sequence is usually done via special characters from a number of sources. This represents a challenge to work with in R and the Biostrings package. The Modstrings package implements this functionallity for RNA and DNA sequences containing modified nucleotides by translating the character internally in order to work with the infrastructure of the Biostrings package. For this the ModRNAString and ModDNAString classes and derivates and functions to construct and modify these objects despite the encoding issues are implemenented. In addition the conversion from sequences to list like location information (and the reverse operation) is implemented as well.
Maintained by Felix G.M. Ernst. Last updated 5 months ago.
dataimportdatarepresentationinfrastructuresequencingsoftwarebioconductorbiostringsdnadna-modificationsmodified-nucleotidesnucleotidesrnarna-modification-alphabetrna-modificationssequences
1 stars 6.64 score 5 scripts 8 dependents
henrikbengtsson
aroma.affymetrix:Analysis of Large Affymetrix Microarray Data Sets
A cross-platform R framework that facilitates processing of any number of Affymetrix microarray samples regardless of computer system. The only parameter that limits the number of chips that can be processed is the amount of available disk space. The Aroma Framework has successfully been used in studies to process tens of thousands of arrays. This package has actively been used since 2006.
Maintained by Henrik Bengtsson. Last updated 1 years ago.
infrastructureproprietaryplatformsexonarraymicroarrayonechannelguidataimportdatarepresentationpreprocessingqualitycontrolvisualizationreportwritingacghcopynumbervariantsdifferentialexpressiongeneexpressionsnptranscriptionaffymetrixanalysiscopy-numberdnaexpressionhpclarge-scalenotebookreproducibilityrna
10 stars 5.79 score 112 scripts 3 dependentsropensci
bold:Interface to Bold Systems API
A programmatic interface to the Web Service methods provided by Bold Systems (<http://www.boldsystems.org/>) for genetic 'barcode' data. Functions include methods for searching by sequences by taxonomic names, ids, collectors, and institutions; as well as a function for searching for specimens, and downloading trace files.
Maintained by Salix Dubois. Last updated 4 months ago.
biodiversitybarcodednasequencesfastaapi-wrapperbarcodestaxize
18 stars 5.74 score 57 scripts
aurora-mareviv
mthapower:Sample Size and Power for Association Studies Involving Mitochondrial DNA Haplogroups
Calculate Sample Size and Power for Association Studies Involving Mitochondrial DNA Haplogroups. Based on formulae by Samuels et al. AJHG, 2006. 78(4):713-720. <DOI:10.1086/502682>.
Maintained by Aurora Baluja. Last updated 6 years ago.
dnageneticshaplogroupmitochondrialsample-size
3 stars 3.18 score 6 scripts
alphaprime7
tidyDenovix:Cleans Spectrophotometry Data Obtained from the Denovix DS-11 Instrument
Cleans spectrophotometry data obtained from the Denovix instrument. The package also provides an option to normalize the data in order to compare the quality of the samples obtained.
Maintained by Tingwei Adeck. Last updated 9 months ago.
data-analysisdnaresearchrnaspectrophotometry
1 stars 2.70 score 2 scripts