Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

ENH: Add new action that can normalize FeatureTable[Frequency] with different methods. #23

Closed
VinzentRisch opened this issue Jan 8, 2024 · 1 comment

Comments

@VinzentRisch
Copy link
Collaborator

VinzentRisch commented Jan 8, 2024

The action annotate-reads-card generates a FeatureTable[Frequency] table. These tables contain the raw information of how many reads were mapped to a certain ARG in CARD. To make meaningful comparisons in and across samples, this information has to be normalized to gene length, library size and composition.

To achieve this, a new action has to be created that can normalize feature tables with current standard methods.
The integration will be done with RNAnorm. A python package that is used for RNAseq normalizations and provides multiple methods like CPM, TPM , FPKM, TMM , CTF, UQ and CUF.

@VinzentRisch VinzentRisch changed the title ENH: Add new action that can normalize FeatureTable[Frequency] with different methods. ENH: Add new action that can normalize FeatureTable[Frequency] with different methods. Feb 9, 2024
@VinzentRisch
Copy link
Collaborator Author

moved to q2-feature-table
qiime2/q2-feature-table#311

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
1 participant