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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.
The text was updated successfully, but these errors were encountered:
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
The action
annotate-reads-card
generates aFeatureTable[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.
The text was updated successfully, but these errors were encountered: