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ilincsapi

https://github.com/uc-bd2k/ilincsapi

Science Score: 44.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (10.1%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Basic Info
  • Host: GitHub
  • Owner: uc-bd2k
  • License: mit
  • Language: HTML
  • Default Branch: master
  • Size: 7.54 MB
Statistics
  • Stars: 9
  • Watchers: 8
  • Forks: 2
  • Open Issues: 2
  • Releases: 4
Created over 7 years ago · Last pushed 11 months ago
Metadata Files
Readme License Citation Zenodo

README.md

ilincsAPI in action

This repository consists of set of examples to showcase the ways of interacting with iLINCS API. The examples in the current folder are implemented in the Jupyter notebook usingIlincsApis.ipynb and "linked" to Google colab.

We also include the same analysis implemented in R markdown -- implemented in the RStudio notebook usingIlincsApis.Rmd and the "knitted" html output of the notebook is provided in usingIlincsApis.html.

Additional R markdown examples are included in subfolders:

Get started

To execute the code in the jupyter notebook, please click on the Google colab and execute code "chunks".

R Markdown

See the same example implemented in R Markdown usingIlincsApis.Rmd

The output is included HTML

R Markdown Prerequisites

To execute the code in the useCase notebooks, please install RStudio, launch RStudio and install following R packages: knitr, tinytex, httr, jsonlite, htmltools, data.table and Biobase.

```R install.packages(c("knitr", "tinytex", "httr", "jsonlite", "htmltools", "data.table"),repos = "http://cran.us.r-project.org") if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager",repos = "http://cran.us.r-project.org");

BiocManager::install("Biobase") ```

Or from shell: sh R -e 'install.packages(c("knitr", "tinytex", "httr", "jsonlite", "htmltools","data.table"),repos = "http://cran.us.r-project.org")' R -e 'if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager",repos = "http://cran.us.r-project.org"); BiocManager::install("Biobase")'

Render in RStudio

After installing the prerequisites and loading Rmd file into RStudio click on "Knit" to create a HTML/Word output.

knitting Rmd file

Render command line

It is also possible to render the usecases using the command line:

  • html output: sh R -e 'rmarkdown::render("usingIlincsApis.Rmd", "html_document")'

Execution time

All scripts execute in less than five minutes on a typical desktop or a laptop computer.

For more information about iLINCS and iLINCS API's see links below:

iLINCS API info page

iLINCS API explorer

iLINCS help

iLINCS support group

Owner

  • Name: uc-bd2k
  • Login: uc-bd2k
  • Kind: organization

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
preferred-citation:
 type: article
 authors:
  - family-names: Pilarczyk
    given-names: Marcin
  - family-names: Fazel-Najafabadi
    given-names: Mehdi
  - family-names: Kouril 
    given-names: Michal
  - family-names: Shamsaei
    given-names: Behrouz
  - family-names: Vasiliauskas
    given-names: Juozas
  - family-names: Niu
    given-names: Wen
  - family-names: Mahi
    given-names: Naim
  - family-names: Zhang
    given-names: Lixia
  - family-names: Clark
    given-names: Nicholas A.
  - family-names: Ren
    given-names: Yan
  - family-names: White
    given-names: Shana
  - family-names: Karim
    given-names: Rashid
  - family-names: Xu
    given-names: Huan
  - family-names: Biesiada
    given-names: Jacek
  - family-names: Bennett
    given-names: Mark F.
  - family-names: Davidson
    given-names: Sarah E.
  - family-names: Reichard
    given-names: John F.
  - family-names: Roberts
    given-names: Kurt
  - family-names: Stathias
    given-names: Vasileios
  - family-names: Koleti
    given-names: Amar
  - family-names: Vidovic
    given-names: Dusica
  - family-names: Clarke
    given-names: Daniel J. B.
  - family-names: Schürer
    given-names: Stephan C.
  - family-names: Ma’ayan
    given-names: Avi
  - family-names: Meller
    given-names: Jarek
  - family-names: Medvedovic
    given-names: Mario
 title: "Connecting omics signatures and revealing biological mechanisms with iLINCS"
 doi: "10.1038/s41467-022-32205-3"
 date-released: 2022-08-09
 journal: "Nature Communications"
 # month: 9
 start: 4678 # First page number
 # end: 10 # Last page number
 issue: 1
 volume: 13
 year: 2022

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