CONP Portal | Dataset


Sharing and reusing gene expression profiling data in neuroscience
Creators: Xian Wan, Tomi Pastinen, Paul Pavlidis
Principal Investigator: Tomi Pastinen
Licenses: CC BY-4.0
Version: 1.0
Formats: PDF
Size: 1.4 MB
No of Files: 2
Primary Publication: Sharing and reusing gene expression profiling data in neuroscience. Xian Wan et al. Scholars Portal Dataverse. https://doi.org/10.5683/SP2/QAIMTK
Metadata file: DATS.json
Other Dates: Release Date: 2019-03-11 00:00:00
Description:
As public availability of gene expression profiling data increases, it is natural to ask how these data can be used by neuroscientists. Here we review the public availability of high-throughput expression data in neuroscience and how it has been reused, and tools that have been developed to facilitate reuse. There is increasing interest in making expression data reuse a routine part of the neuroscience tool-kit, but there are a number of challenges. Data must become more readily available in public databases; efforts to encourage investigators to make data available are important, as is education on the benefits of public data release. Once released, data must be better-annotated. Techniques and tools for data reuse are also in need of improvement. Integration of expression profiling data with neuroscience-specific resources such as anatomical atlases will further increase the value of expression data. (2018-02)

Dataset README information

Download Using DataLad

CircleCI status

The following instructions require a basic understanding of UNIX/LINUX command lines. A subset of open datasets on the Portal are also available through a browser-based download button. The instructions below regard dataset download with the use of DataLad. To install DataLad on your system, please refer to the install section of the DataLad Handbook .

Note: For maximum compatibility with conp-dataset, the CONP recommends versions 3.12+ of Python, 10.20241202+ of git-annex, and 1.1.4+ of datalad.

1) Initiate the CONP dataset

Run the following command in the directory where you want the CONP dataset (conp-dataset) to be installed:

2) Install the Reusing-Neuro-Data dataset

To install the Reusing-Neuro-Data dataset, run the following commands to move into the "projects" subdirectory under the "conp-dataset" directory (created in the previous step) and run datalad install:

3) Download data from the Reusing-Neuro-Data dataset

Now that the dataset has been installed, go into the Reusing-Neuro-Data dataset directory.

The files visible after installing the dataset but before downloading (in the next step) are symbolic links and need to be downloaded manually using the datalad get command:

If you run datalad get * command, all the files available in the dataset directory will be downloaded.


For more information on how DataLad works, please visit the DataLad Handbook documentation.