https://github.com/applicativesystem/pangenome-metagenomics

pangenome metagenomics normlization for specific ids
https://github.com/applicativesystem/pangenome-metagenomics

bioinformatics genome-analysis genome-annotation genome-informatics metagenomics metagenomics-binning metagenomics-counts metagenomics-data

Last synced: 7 days ago
JSON representation

pangenome metagenomics normlization for specific ids

• Host: GitHub
• URL: https://github.com/applicativesystem/pangenome-metagenomics
• Owner: applicativesystem
• License: mit
• Created: 2024-08-26T09:34:01.000Z (4 months ago)
• Default Branch: main
• Last Pushed: 2024-08-26T09:36:30.000Z (4 months ago)
• Last Synced: 2024-11-10T20:18:15.443Z (about 1 month ago)
• Topics: bioinformatics, genome-analysis, genome-annotation, genome-informatics, metagenomics, metagenomics-binning, metagenomics-counts, metagenomics-data
• Language: Python
• Homepage:
• Size: 94.7 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

        
# pangenomeMetagenomicsNormalizer

- takes a presence absence file of metagenomics and then sum the presence absence across the species and then divide it with the number of the gene ontology plus child categories included and presents you a ratio.

- The higher the ratio means that the ontology is distributed well across all the species.

```

pangenomeMetagenomicsNormalize("/Users/gauravsablok/Desktop/CodeCheck/csv_test_datasets/Pangenome.csv")

	go_category	effectsize

0	atp-dependent clp atp-binding subunit	34.50

1	dna a subunit	13.29

2	dna gyrase subunit b	11.50

3	phospho-2-dehydro-3-deoxyheptonate aldolase	17.40

4	6-phospho-beta-glucosidase	27.33

...	...	...

1656	nucleotidyltransferase domain	1.00

1657	sodium-dependent phosphate transporter	0.10

1658	adenine-specific dna-methyltransferase ed	0.25

```

Gaurav Sablok \

University of Potsdam \

Potsdam,Germany