Releases: solislemuslab/minaa
v1.2.0
MiNAA v1.2.0
Feature: Conserved Subgraph Identification
Given a pair of graphs G and H and an alignment on them, we define a conserved subgraph as a connected subgraph of G whose nodes are aligned to a connected subgraph of H. For more information see the Examples section of the main README.
New Argument:
-c: conserved subgraphs; whether or not to output a list of the conserved subgraphs in the alignment between G and H. Feature: Alignment Visualization
We provide a modest R script for alignment visualization. See Example 4 in examples/README.md for more info. We intend to eventually supply a more sophisticated and interactive method in the to-be-developed MiNAA Webapp.
v1.1.0
MiNAA v1.1.0
Overview
This update brings a large number of peripheral changes to MiNAA which enhance user experience and understanding, code readability, and the ability to interface with other programs. Core functionality has not changed at all. Any commands and inputs previously run on version 1.0.1 will work and output the same results.
New Optional Arguments
- -st=: similarity threshold; the similarity value above which aligned pairs are included in the output.
- Require: a real number in range [0, 1].
- Default: 0.
- Note: for computational complexity reasons, MiNAA finds a complete matching between two networks. This means that certain nodes may be matched by the algorithm, even if they obviously bear no relation (have a very low similarity). This functionality ameliorates that.
- -Galias=: an alias for the G file.
- Require: a valid file name.
- Default: the G file keeps its original name.
- -Halias=: an alias for the H file.
- Require: a valid file name.
- Default: the H file keeps its original name.
- -Balias=: an alias for the B file.
- Require: a valid file name.
- Default: the B file keeps its original name.
- -p: passthrough; whether or not to write the input files into the output folder.
- Require: none.
- Default: the files are not passed through to the output folder.
- Note: The output reflects the input data after having been processed by the algorithm, this is not a direct copy and paste.
- -t: timestamp; the output folder's name includes the date and time of execution.
- Require: none.
- Default: the output folder's name does not include date and time.
- -g: greekstamp; the output folder's name includes the values for alpha and beta.
- Require: none.
- Default: the output folder's name does not include the values for alpha and beta.
- -s: similarity conversion; for each entry in the given biological matrix, the value (post normalization) is replaced with 1 - value.
- Require: none.
- Default: the given biological matrix is left as is.
- Note: use this if and only if the provided biological matrix is a similarity matrix.
Additional Changes
- The new
examplesdirectory contains several examples incorporating the existing and new arguments, using data derived from a real microbiome. - All documentation has been updated in accordance with the changes described here.
- The source code has undergone refactoring and reformatting for readability and maintainability reasons.