Question: What Computational Tools Specialize in Human Cell Types?
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gravatar for Trombone Engineer
2.2 years ago by
Trombone Engineer0 wrote:

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?

ADD COMMENTlink modified 2.2 years ago by Samuel Brady300 • written 2.2 years ago by Trombone Engineer0
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gravatar for Jean-Karim Heriche
2.2 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche20k wrote:

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.

ADD COMMENTlink written 2.2 years ago by Jean-Karim Heriche20k
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gravatar for Samuel Brady
2.2 years ago by
Samuel Brady300
Samuel Brady300 wrote:

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.

ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by Samuel Brady300
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