Specialize diffexp for tiledb (#1384)

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* Specialize diffexp for tiledb

This patch adds a new diffexp algorithm which is tuned for tiledb.
This algorithm was written by Bruce and is adapted here to plug into the
current framework.  The anndata_adaptor still calls the original
algotithm (which was move from diffexp.py to diffexp_generic.py).
The cxg_adaptor now calls the new diffexp_tiledb version.  Some
code is shared between the two.

This is part 1 of the diffexp for tiledb.  Further tuning and
global throttles are still needed.

A script to run and time diffexp with various options is also
added: test/run_diffexp.py.

This commit is contained in:

bmccandless

2020-04-12 09:56:55 -07:00

committed by

GitHub

parent 5dcfcb5467

commit 98c2a1359b

10 changed files with 328 additions and 86 deletions

									
										server/common/default_config.py
									
		+1
		
												View File
												
				@@ -65,6 +65,7 @@ embeddings:

				diffexp:

				  enable: true

				  lfc_cutoff: 0.01

				  top_n: 10

				data_locator:

				  s3: