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What Computational Tools Specialize in Human Cell Types?

What Computational Tools Specialize in Human Cell Types? I do a fair amount of genomic and metagenomic analysis on microbiome datasets as well as human data and conclusions from other studies. What computational tools exist that can specialize in genomic inference specific to a single type of human cell? I am most interested in mast cells and goblet cells. I have found the Human Protein Atlas to be an extremely useful resource that processes tissue specific expression from RNASeq data (as far as I understand) into relative expression levels of various genes across human tissues. What else exists to profile or view curated knowledge on active portions of the genome within cell types such as goblet cells or mast cells?

genome alignment gene cell type human
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updated by Samuel Brady Samuel Brady • written by Trombone Engineer • Trombone Engineer

2 answers

Have a look at the Expression Atlas. The ENCODE experiments on cells and tissues are available there but there may be others. I don't know if they have anything about your favourite cells though.

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written by Jean-Karim Heriche Jean-Karim Heriche

xCell aims to identify cell types based on expression data. It may work for your needs. The paper is here. You can see in Figure 1B that xCell does work for mast cells. Figure 2C shows comparisons between xCell and 6 other tools you could also consider trying.

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written by Samuel Brady Samuel Brady

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