TACITuS: transcriptomic data collector, integrator, and selector on big data platform
Abstract Background Several large public repositories of microarray datasets and RNA-seq data are available. Two prominent examples include ArrayExpress and NCBI GEO. Unfortunately, there is no easy way to import and manipulate data from such resources, because the data is stored in large files, req...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2019-11-01
|
| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12859-019-2912-4 |
| _version_ | 1828958252876955648 |
|---|---|
| author | Salvatore Alaimo Antonio Di Maria Dennis Shasha Alfredo Ferro Alfredo Pulvirenti |
| author_facet | Salvatore Alaimo Antonio Di Maria Dennis Shasha Alfredo Ferro Alfredo Pulvirenti |
| author_sort | Salvatore Alaimo |
| collection | DOAJ |
| description | Abstract Background Several large public repositories of microarray datasets and RNA-seq data are available. Two prominent examples include ArrayExpress and NCBI GEO. Unfortunately, there is no easy way to import and manipulate data from such resources, because the data is stored in large files, requiring large bandwidth to download and special purpose data manipulation tools to extract subsets relevant for the specific analysis. Results TACITuS is a web-based system that supports rapid query access to high-throughput microarray and NGS repositories. The system is equipped with modules capable of managing large files, storing them in a cloud environment and extracting subsets of data in an easy and efficient way. The system also supports the ability to import data into Galaxy for further analysis. Conclusions TACITuS automates most of the pre-processing needed to analyze high-throughput microarray and NGS data from large publicly-available repositories. The system implements several modules to manage large files in an easy and efficient way. Furthermore, it is capable deal with Galaxy environment allowing users to analyze data through a user-friendly interface. |
| first_indexed | 2024-12-14T08:45:38Z |
| format | Article |
| id | doaj.art-d19db2b177234bbb84aee8a55faac0db |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-14T08:45:38Z |
| publishDate | 2019-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-d19db2b177234bbb84aee8a55faac0db2022-12-21T23:09:12ZengBMCBMC Bioinformatics1471-21052019-11-0120S911110.1186/s12859-019-2912-4TACITuS: transcriptomic data collector, integrator, and selector on big data platformSalvatore Alaimo0Antonio Di Maria1Dennis Shasha2Alfredo Ferro3Alfredo Pulvirenti4Department of Clinical and Experimental Medicine, University of CataniaDepartment of Clinical and Experimental Medicine, University of CataniaCourant Institute of Mathematical Science, New York UniversityDepartment of Clinical and Experimental Medicine, University of CataniaDepartment of Clinical and Experimental Medicine, University of CataniaAbstract Background Several large public repositories of microarray datasets and RNA-seq data are available. Two prominent examples include ArrayExpress and NCBI GEO. Unfortunately, there is no easy way to import and manipulate data from such resources, because the data is stored in large files, requiring large bandwidth to download and special purpose data manipulation tools to extract subsets relevant for the specific analysis. Results TACITuS is a web-based system that supports rapid query access to high-throughput microarray and NGS repositories. The system is equipped with modules capable of managing large files, storing them in a cloud environment and extracting subsets of data in an easy and efficient way. The system also supports the ability to import data into Galaxy for further analysis. Conclusions TACITuS automates most of the pre-processing needed to analyze high-throughput microarray and NGS data from large publicly-available repositories. The system implements several modules to manage large files in an easy and efficient way. Furthermore, it is capable deal with Galaxy environment allowing users to analyze data through a user-friendly interface.http://link.springer.com/article/10.1186/s12859-019-2912-4RNA-SeqCloud storage and managementGalaxy |
| spellingShingle | Salvatore Alaimo Antonio Di Maria Dennis Shasha Alfredo Ferro Alfredo Pulvirenti TACITuS: transcriptomic data collector, integrator, and selector on big data platform BMC Bioinformatics RNA-Seq Cloud storage and management Galaxy |
| title | TACITuS: transcriptomic data collector, integrator, and selector on big data platform |
| title_full | TACITuS: transcriptomic data collector, integrator, and selector on big data platform |
| title_fullStr | TACITuS: transcriptomic data collector, integrator, and selector on big data platform |
| title_full_unstemmed | TACITuS: transcriptomic data collector, integrator, and selector on big data platform |
| title_short | TACITuS: transcriptomic data collector, integrator, and selector on big data platform |
| title_sort | tacitus transcriptomic data collector integrator and selector on big data platform |
| topic | RNA-Seq Cloud storage and management Galaxy |
| url | http://link.springer.com/article/10.1186/s12859-019-2912-4 |
| work_keys_str_mv | AT salvatorealaimo tacitustranscriptomicdatacollectorintegratorandselectoronbigdataplatform AT antoniodimaria tacitustranscriptomicdatacollectorintegratorandselectoronbigdataplatform AT dennisshasha tacitustranscriptomicdatacollectorintegratorandselectoronbigdataplatform AT alfredoferro tacitustranscriptomicdatacollectorintegratorandselectoronbigdataplatform AT alfredopulvirenti tacitustranscriptomicdatacollectorintegratorandselectoronbigdataplatform |