Cell SubTypes 47/ 53 classes : How?
How did you define cell subtypes 47/53 from Cell Subtype column 'obs cl295v11SubFull' of GSE178341
dataset I can see there are 87 unique cell subtypes. Could you please clarify, how did you choose 47/53 subtypes here ?
Thank you for your question. Some of the cell types were consolidated to match other data sources we are using for ongoing work. For example, all B cell subtypes were consolidated into B cells.
This is not not clear in the paper
Could you please explain it here ?
This is not not clear in the paper
Could you please explain it here ?
Even though consolidating all B subtypes into B cells, I am still left with 84 subtypes,
I can see only 3 b types cB1, cB2 and cB3. from column 'cl295v11SubShort'
anndata.obs.cl295v11SubShort.unique()
{'cTNI15', 'cM05', 'cTNI22', 'cB2', 'cE05', 'cTNI08', 'cTNI19', 'cTNI11', 'cS11', 'cE02', 'cS05', 'cP3', 'cS04', 'cTNI06', 'cM10', 'cTNI12', 'cP1', 'cTNI10', 'cTNI05', 'cM06', 'cS07', 'cE09', 'cE04', 'cE06', 'cTNI24', 'cTNI14', 'cS26', 'cTNI26', 'cTNI02', 'cS23', 'cS15', 'cTNI18', 'cS17', 'cS08', 'cB3', 'cS14', 'cM09', 'cE07', 'cS30', 'cTNI20', 'cM04', 'cM03', 'cS19', 'cM02', 'cS31', 'cS28', 'cS27', 'cS03', 'cTNI17', 'cE01', 'cTNI13', 'cM01', 'cS20', 'cP2', 'cS29', 'cS13', 'cE11', 'cTNI16', 'cS09', 'cS25', 'cS10', 'cS02', 'cTNI25', 'cM08', 'cTNI04', 'cM07', 'cS16', 'cS21', 'cE08', 'cMA01', 'cTNI01', 'cE10', 'cTNI07', 'cTNI09', 'cS01', 'cS06', 'cE03', 'cTNI23', 'cS18', 'cS22', 'cS12', 'cB1', 'cS33', 'cS32', 'cTNI21', 'cS24', 'cTNI03'}
This is one example where cell types were consolidated. Other cell types were also consolidated. This discussion page is for discussions related to the code on this repository. If you have further questions regarding the biological analyses in the paper, please email. Thank you!