Oasis: online analysis of small RNA deep sequencing data.


Oasis is a web application that allows for the fast and flexible online analysis of small-RNA-seq (sRNA-seq) data. It was designed for the end user in the lab, providing an easy-to-use web frontend including video tutorials, demo data and best practice step-by-step guidelines on how to analyze sRNA-seq data. Oasis' exclusive selling points are a differential expression module that allows for the multivariate analysis of samples, a classification module for robust biomarker detection and an advanced programming interface that supports the batch submission of jobs. Both modules include the analysis of novel miRNAs, miRNA targets and functional analyses including GO and pathway enrichment. Oasis generates downloadable interactive web reports for easy visualization, exploration and analysis of data on a local system. Finally, Oasis' modular workflow enables for the rapid (re-) analysis of data.

 One problem is that it only support a few species:
Mus musculus - mm10
Homo sapiens - hg19
Drosophila melanogaster - dm3
Danio Rerio - zc19
Caenorhabditis elegans - ce10

Plant species were not included. 

References
https://oasis.dzne.de/index.php

Comments

Post a Comment

Popular posts from this blog

gspread error:gspread.exceptions.SpreadsheetNotFound

Error message: Traceback (most recent call last):   File "read_google_sheet.py", line 20, in <module>     wks = gc.open_by_key("1jUJOlICOH6VnyuALdU2VAc_Ci_ZVwdW-xc5kr_qkJHY")   File "/usr/lib/python2.7/site-packages/gspread/client.py", line 113, in open_by_key     raise SpreadsheetNotFound gspread.exceptions.SpreadsheetNotFound Solved : In the json file, there is a "client_email". You need to share your file with this email. 
Read more

Miniconda installation problem: concurrent.futures.process.BrokenProcessPool: A process in the process pool was terminated abruptly while the future was running or pending.

We got error message shown as below: [/home/omicsacademy/miniconda3] >>> PREFIX=/home/omicsacademy/miniconda3 Unpacking payload ... concurrent.futures.process._RemoteTraceback: ''' Traceback (most recent call last):   File "concurrent/futures/process.py", line 368, in _queue_management_worker   File "multiprocessing/connection.py", line 251, in recv TypeError: __init__() missing 1 required positional argument: 'msg' ''' The above exception was the direct cause of the following exception: Traceback (most recent call last):   File "entry_point.py", line 69, in <module>   File "concurrent/futures/process.py", line 484, in _chain_from_iterable_of_lists   File "concurrent/futures/_base.py", line 611, in result_iterator   File "concurrent/futures/_base.py", line 439, in result   File "concurrent/futures/_base.py", line 388, in __get_result concurrent.futures.process.BrokenProc...
Read more

P and q values in RNA Seq

The q-value is an adjusted p-value, taking in to account the false discovery rate (FDR). Applying a FDR becomes necessary when we're measuring thousands of variables (e.g. gene expression levels) from a small sample set (e.g. a couple of individuals). A p-value of 0.05 implies that we are willing to accept that 5% of all tests will be false positives. An FDR-adjusted p-value (aka a q-value) of 0.05 implies that we are willing to accept that 5% of the tests found to be statistically significant (e.g. by p-value) will be false positives. Such an adjustment is necessary when we're making multiple tests on the same sample. See, for example, http://www.totallab.com/products/samespots/support/faq/pq-values.aspx. -HomeBrew What are p-values? The object of differential 2D expression analysis is to find those spots which show expression difference between groups, thereby signifying that they may be involved in some biological process of interest to the researcher. Due to chance, the...
Read more