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alexpate30
rcprd:Extraction and Management of Clinical Practice Research Datalink Data
Simplify the process of extracting and processing Clinical Practice Research Datalink (CPRD) data in order to build datasets ready for statistical analysis. This process is difficult in 'R', as the raw data is very large and cannot be read into the R workspace. 'rcprd' utilises 'RSQLite' to create 'SQLite' databases which are stored on the hard disk. These are then queried to extract the required information for a cohort of interest, and create datasets ready for statistical analysis. The processes follow closely that from the 'rEHR' package, see Springate et al., (2017) <doi:10.1371/journal.pone.0171784>.
Maintained by Alexander Pate. Last updated 11 hours ago.
2 stars 5.53 score 5 scripts
bioc
regutools:regutools: an R package for data extraction from RegulonDB
RegulonDB has collected, harmonized and centralized data from hundreds of experiments for nearly two decades and is considered a point of reference for transcriptional regulation in Escherichia coli K12. Here, we present the regutools R package to facilitate programmatic access to RegulonDB data in computational biology. regutools provides researchers with the possibility of writing reproducible workflows with automated queries to RegulonDB. The regutools package serves as a bridge between RegulonDB data and the Bioconductor ecosystem by reusing the data structures and statistical methods powered by other Bioconductor packages. We demonstrate the integration of regutools with Bioconductor by analyzing transcription factor DNA binding sites and transcriptional regulatory networks from RegulonDB. We anticipate that regutools will serve as a useful building block in our progress to further our understanding of gene regulatory networks.
Maintained by Joselyn Chavez. Last updated 4 months ago.
generegulationgeneexpressionsystemsbiologynetworknetworkinferencevisualizationtranscriptionbioconductorcdsbregulondb
4 stars 5.20 score 6 scripts
nononoexe
roadnetdb:Package for road network operation with pgRouting
This package provides functions for road network operation with pgRouting.
Maintained by Keisuke ANDO. Last updated 7 months ago.
1.70 score 2 scripts