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# update tutorials
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kullrich committed Sep 21, 2023
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Expand Up @@ -12,15 +12,15 @@ over all evolutionary age categories denoted as *phylostra*.

.. math::
eqn{TEI_s = sum (e_is * ps_i) / sum e_is}
TEI_s = sum (e_is * ps_i) / sum e_is
where :math:`eqn{TEI_s}` denotes the TEI value in developmental stage
:math:`eqn{s, e_is}` denotes the gene expression level of gene :math:`eqn{i}`
in stage :math:`eqn{s}`, and :math:`eqn{ps_i}` denotes the corresponding phylostratum
of gene :math:`eqn{i, i = 1,…,N}` and :math:`eqn{N = total number of genes}`.
where :math:`TEI_s` denotes the TEI value in developmental stage
:math:`s, e_is` denotes the gene expression level of gene :math:`i`
in stage :math:`s`, and :math:`eqn{ps_i}` denotes the corresponding phylostratum
of gene :math:`i, i = 1,…,N` and :math:`N = total number of genes`.

.. note::
Please have a look at `Liu & Robinson-Rechavi, 2018<https://doi.org/10.1093/gbe/evy177>`_ to get more insides how expression transformation can influence TEI calculation.
Please have a look at `Liu & Robinson-Rechavi, 2018 <https://doi.org/10.1093/gbe/evy177>`_ to get more insides how expression transformation can influence TEI calculation.
By default, the expression values are pre-processed. This includes normalizing the counts per cell (see option `normalize_total`) to a total count of 1e6 (which corresponds to CPM; see option `target_sum`) and log-transformed (see option `log1p`).

How to add a transcriptome evolutionary index (short: TEI) to scRNA data
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