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Describe the goals of the changes to the analysis module.
In the next PR, I would like to write a notebook that will provide the first annotations for the Wilms tumor dataset SCPCP000006.
The proposed annotation will be base on the combination of:
the label transfer fron the fetal kidney reference (Stewart et al.), in particular the fetal_kidney_predicted.compartment and fetal_kidney:predicted.cell_type, as well as the mapping.score for each compartment,
the predicted CNV calculated using intra-sample endothelial and immune cells (--reference both) as normal reference
We will then use some of the markers genes to validate visually the annotations.
If you are filing this issue based on a specific GitHub Discussion, please link to the relevant Discussion.
No response
Describe the goals of the changes to the analysis module.
In the next PR, I would like to write a notebook that will provide the first annotations for the Wilms tumor dataset SCPCP000006.
The proposed annotation will be base on the combination of:
fetal_kidney_predicted.compartmentandfetal_kidney:predicted.cell_type, as well as themapping.scorefor each compartment,--reference both) as normal referenceWe will then use some of the markers genes to validate visually the annotations.
The analysis can be summarized as the following:
cnv.thrandmap.thrneed to be discussed.<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:x="urn:schemas-microsoft-com:office:excel" xmlns="http://www.w3.org/TR/REC-html40">
first level annotation | second level annotation | selection of the cells | marker genes for validation | cnv validation -- | -- | -- | -- | -- normal | endothelial | compartment == "endothelium" & mapping_score > map.thr & cnv_score < cnv.thr | WVF | no cnv normal | immune | compartment == "immune" & mapping_score > map.thr & cnv_score < cnv.thr | PTPRC, CD163, CD68 | no cnv normal | kidney | cell_type %in% c("kidney cell", "kidney epithelial", "podocyte") & mapping_score > map.thr & cnv_score < cnv.thr | CDH1, PODXL, LTL | no cnv normal | stroma | compartment == "stroma" & mapping_score > map.thr & cnv_score < cnv.thr | VIM | no cnv cancer | stroma | compartment == "stroma" & cnv_score > cnv.thr | VIM | proportion_cnv_chr -1 -4 -11 -16 -17 -18 cancer | blastema | compartment == "fetal_nephron" & cell_type == "mesenchymal cell" & cnv_score > cnv.thr | CITED1 | proportion_cnv_chr -1 -4 -11 -16 -17 -18 cancer | epithelial | compartment == "fetal_nephron" & cell_type != "mesenchymal cell" & cnv_score > cnv.thr | CDH1 | proportion_cnv_chr -1 -4 -11 -16 -17 -18 unknown | - | the rest of the cells | - | proportion_cnv_chr -1 -4 -11 -16 -17 -18