https://github.com/jefferis/flynblastscores
R package to provide RESTful interface via opencpu to NBLAST scores for fly neurons
https://github.com/jefferis/flynblastscores
Last synced: 3 months ago
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R package to provide RESTful interface via opencpu to NBLAST scores for fly neurons
- Host: GitHub
- URL: https://github.com/jefferis/flynblastscores
- Owner: jefferis
- Created: 2015-11-13T03:31:38.000Z (over 9 years ago)
- Default Branch: master
- Last Pushed: 2020-06-22T12:35:52.000Z (almost 5 years ago)
- Last Synced: 2025-01-16T03:33:39.206Z (4 months ago)
- Language: R
- Homepage: http://jefferis.github.io/flynblastscores
- Size: 40 KB
- Stars: 0
- Watchers: 1
- Forks: 1
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- Changelog: NEWS.md
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README
# flynblastscores
R package to provide RESTful interface via opencpu to NBLAST scores for fly neurons
## Introduction
This package provides functions to simplify access to pre-computed
[NBLAST](jefferislab.org/si/nblast) scores for fly neurons. There are two main
functions of interest
`flycircuit_topn` returns scores for self-match queries for
[flycircuit](http://flycircuit.tw) neurons.
`flycircuit_gmr_topn` returns scores for querying flycircuit neurons againt a
processed version of the [GMR Gal4 lines](http://flweb.janelia.org/cgi-bin/flew.cgi).
These functions can be used in any classic R environment or as the basis of
a RESTful interface through the [opencpu](http://opencpu.org) API.
## Installation
Note that installing/using this package will trigger a one time download of about 1.5 Gb
of pre-computed NBLAST scores.
Currently there isn't a released version on [CRAN](http://cran.r-project.org/),
but you can use the **devtools** [1] package to install the development version:
```r
if (!require("devtools")) install.packages("devtools")
devtools::install_github("jefferis/flynblastscores")
# You may also want to install the suggested package vfbr to interact with
# resources on the virtual fly brain website
devtools::install_github("jefferis/vfbr")
```
## Use
See
http://vfbdev.inf.ed.ac.uk/ocpu/library/flynblastscores/man/flycircuit_topn
for more information
## Acknowledgements
Please be sure to cite the original data sources
* flycircuit.tw
* flweb.janelia.org/cgi-bin/flew.cgi
as well as the paper (currently available as a
[biorxiv preprint](http://dx.doi.org/10.1101/006346)) describing the
NBLAST algorithm if you use this package / data in published work.