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Addition Description
When creating a FeatureTable[Frequency] by mapping reads to reference genes, the resulting data is total amount of reads that mapped to a gene. With this data it is impossible to make comparisons inside a sample, because of different gene lengths and it is also impossible to make comparisons between samples because of different total amount of reads per sample. To solve this issue I propose a new action that can normalize the tables with various methods. The python package used for this action will be RNAnorm.
The action will take as inputs FeatureTable[Frequency] and SequenceCharacteristics[Length]. And it will output FeatureTable[Normalized], that will be added to q2-types with qiime2/q2-types#339.
There will be properties added to the output indicating the method used.
VinzentRisch
changed the title
ENH: Adding new type called FeatureTable[Normalized]
ENH: Adding new action to normalize FeatureTable[Frequency]
Jul 19, 2024
Addition Description
When creating a
FeatureTable[Frequency]
by mapping reads to reference genes, the resulting data is total amount of reads that mapped to a gene. With this data it is impossible to make comparisons inside a sample, because of different gene lengths and it is also impossible to make comparisons between samples because of different total amount of reads per sample. To solve this issue I propose a new action that can normalize the tables with various methods. The python package used for this action will be RNAnorm.The action will take as inputs
FeatureTable[Frequency]
andSequenceCharacteristics[Length]
. And it will output FeatureTable[Normalized], that will be added to q2-types with qiime2/q2-types#339.There will be properties added to the output indicating the method used.
See here for details on the different methods.
References
https://forum.qiime2.org/t/2024-07-03-group-meeting/30649/5
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