Analysis code and derived data for: CLEC10A marks an MHC class II-high tumour myeloid state that lies in T-cell-rich neighbourhoods, and its survival association is seen in MYCN non-amplified neuroblastoma

Analysis code and derived data behind every figure and statistic in the manuscript CLEC10A marks an MHC class II-high tumour myeloid state that lies in T-cell-rich neighbourhoods, and its survival association is seen in MYCN non-amplified neuroblastoma. The deposit contains no primary sequencing data. All primary data are already public: GEO GSE85047, GSE62564, GSE147766 and GSE332618, and the NCI TARGET-NBL programme. Two things here cannot be regenerated from the code alone and are the reason the deposit exists in this form: the matched-pair assignments, because matching draws controls at random within strata, and the pre-correction outputs, which let a reader see exactly what the depth and composition corrections changed. Grouping cells or bins by detection of a marker puts sequencing depth into the definition of the groups, and the deposit documents the before state as well as the result: 395 significant genes become 107, and a MYC-targets enrichment of NES 2.14 (q<0.001) disappears to NES 1.29 (q=0.83). Contents: analysis code for the bulk survival, single-cell and spatial analyses and for figure assembly; per-panel numeric source data; matched-cell and matched-bin assignments; superseded pre-correction outputs; quality-control records; and Supplementary Tables S1-S11 as published. Licences. Code in 01_code/ is released under the MIT Licence (LICENSE-MIT.txt); the derived data files are released under CC BY 4.0 (LICENSE-DATA.txt). Primary data remain under the terms of their original repositories and are not redistributed here. This research received no specific grant from any funding agency in the public, commercial or not-for-profit sectors. The authors declare no competing interests.