Practical machine learning examples in biology






Classification of Lung cancer slide images using deep-learning: https://github.com/ncoudray/DeepPATH\

CANDLE:

REVOLVER - Repeated Evolution in Cancer: https://github.com/caravagn/revolver

Markerless tracking of user-defined features with deep learning: https://github.com/AlexEMG/DeepLabCut












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

Update the TOC (table of content) of MS Word .docx documents with Python

Here is a snippet to update the TOC of a word 2013 .docx document which includes only one table of content (e.g. just TOC of headings, no TOC of figures etc.). If the script  update_toc.py  is run from the command promt (windows 10, command promt not "running as admin") using  python update_toc.py  the system installation of python opens the file  doc_with_toc.docx  in the same directory, updates the TOC (in my case the headings) and saves the changes into the same file. The document may not be opened in another instance of Word 2013 and may not be write-protected. Be aware of that this script does  not the same as selecting the whole document content and pressing the F9 key . Content of  update_toc.py : import win32com . client import inspect , os def update_toc ( docx_file ): word = win32com . client . DispatchEx ( "Word.Application" ) doc = word . Documents . Open ( docx_file ) doc . TablesOfContents ( 1 ). Update () ...
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