pubtatordb - Create and Query a Local 'PubTator' Database

'PubTator' <https://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/PubTator/> is a National Center for Biotechnology Information (NCBI) tool that enhances the annotation of articles on PubMed <https://www.ncbi.nlm.nih.gov/pubmed/>. It makes it possible to rapidly identify potential relationships between genes or proteins using text mining techniques. In contrast, manually searching for and reading the annotated articles would be very time consuming. 'PubTator' offers both an online interface and a RESTful API, however, neither of these approaches are well suited for frequent, high-throughput analyses. The package 'pubtatordb' provides a set of functions that make it easy for the average R user to download 'PubTator' annotations, create, and then query a local version of the database.

Last updated 5 years ago

annotationbiologypubmed

3.90 score 16 scripts 145 downloads

Bioi - Biological Image Analysis

Single linkage clustering and connected component analyses are often performed on biological images. 'Bioi' provides a set of functions for performing these tasks. This functionality is implemented in several key functions that can extend to from 1 to many dimensions. The single linkage clustering method implemented here can be used on n-dimensional data sets, while connected component analyses are limited to 3 or fewer dimensions.

Last updated 5 years ago

biological-data-analysisbiologycellcppimage-analysismicroscopy

3.81 score 13 scripts 192 downloads

documenter - Documents Files

It is sometimes necessary to create documentation for all files in a directory. Doing so by hand can be very tedious. This task is made fast and reproducible using the functionality of 'documenter'. It aggregates all text files in a directory and its subdirectories into a single word document in a semi-automated fashion.

Last updated 2 years ago

documentationdocx

3.70 score 1 stars 10 scripts 175 downloads

disttools - Distance Object Manipulation Tools

Provides convenient methods for accessing the data in 'dist' objects with minimal memory and computational overhead. 'disttools' can be used to extract the distance between any pair or combination of points encoded by a 'dist' object using only the indices of those points. This is an improvement over existing functionality, which requires either coercing a 'dist' object into a matrix or calculating the one dimensional index corresponding to a pair of observations. Coercion to a matrix is undesirable because doing so doubles the amount of memory required for storage. In contrast, there is no inherent downside to the latter solution. However, in part due to several edge cases, correctly and efficiently implementing such a solution can be challenging. 'disttools' abstracts away these challenges and provides a simple interface to access the data in a 'dist' object using the latter approach.

Last updated 3 years ago

distance

3.70 score 4 scripts 166 downloads