Posts with the "data access" tag
restez: Query GenBank locally
December 3, 2018
What is restez? R packages for interacting with the National Center for Biotechnology Information (NCBI) have, to-date, depended on API query calls via NCBI’s Entrez. For computational analyses that require the automated look-up of reams of biological sequence data, piecemeal querying via bandwith-limited requests is evidently not ideal. These queries are not only slow, but they depend on network connections and the remote server’s consistent behaviour. Additionally, users who make very large requests over extended periods of time run the risk of being blocked.
Mapping the 2018 East Africa floods from space with smapr
September 25, 2018
Hundreds of thousands of people in east Africa have been displaced and hundreds have died as a result of torrential rains which ended a drought but saturated soils and engorged rivers, resulting in extreme flooding in 2018. This post will explore these events using the R package smapr, which provides access to global satellite-derived soil moisture data collected by the NASA Soil Moisture Active-Passive (SMAP) mission and abstracts away some of the complexity associated with finding, acquiring, and working with the HDF5 files that contain the observations (shout out to Laura DeCicco and Marco Sciaini for reviewing smapr, and Noam Ross for editing in the rOpenSci onboarding process).
phylotaR: Retrieve Orthologous Sequences from GenBank
August 8, 2018
In this technote I will outline what phylotaR was developed for, how to install it and how to run it with some simple examples.
What is phylotaR? In any phylogenetic analysis it is important to identify sequences that share the same orthology – homologous sequences separated by speciation events. This is often performed by simply searching an online sequence repository using sequence labels. Relying solely on sequence labels, however, can miss sequences that have either not been labelled, have unanticipated names or have been mislabelled.
Extracting and Processing eBird Data
August 7, 2018
eBird is an online tool for recording bird observations. The eBird database currently contains over 500 million records of bird sightings, spanning every country and nearly every bird species, making it an extremely valuable resource for bird research and conservation. These data can be used to map the distribution and abundance of species, and assess how species’ ranges are changing over time. This dataset is available for download as a text file; however, this file is huge (over 180 GB!
treeio: Phylogenetic data integration
May 17, 2018
Phylogenetic trees are commonly used to present evolutionary relationships of species. Newick is the de facto format in phylogenetic for representing tree(s). Nexus format incorporates Newick tree text with related information organized into separated units known as blocks. For the R community, we have ape and phylobase packages to import trees from Newick and Nexus formats. However, analysis results (tree + analysis findings) from widely used software packages in this field are not well supported.