PMC:7417788 / 66946-67739 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7417788","sourcedb":"PMC","sourceid":"7417788","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7417788","text":"Dimensionality reduction and clustering analysis of scRNA-seq datasets\nTo analyze the scRNA-seq data, we log normalized data (1 + counts per 10,000) with the ‘‘sc.pp.normalize_total’’ function before clustering, reduction and performing 2-dimensional t-SNE algorithm clustering with the first 50 principal components. This was done following PCA on top 5,000 most variable genes by using “sc.pp.highly_variable_genes” function in Scanpy with the default parameters. Dimensionality method and identification of significant clusters and was performed using Leiden clustering algorithm which uses a shared nearest neighbour modularity optimization-based clustering algorithm. Marker genes for each significant cluster were found using the function sc.tl.rank_genes_groups with default parameters.","divisions":[{"label":"title","span":{"begin":0,"end":70}}],"tracks":[{"project":"LitCovid-PMC-OGER-BB","denotations":[{"id":"T1445","span":{"begin":86,"end":91},"obj":"SO:0002031"},{"id":"T1446","span":{"begin":373,"end":378},"obj":"SO:0000466"},{"id":"T1447","span":{"begin":411,"end":416},"obj":"SO:0000466"},{"id":"T1448","span":{"begin":680,"end":685},"obj":"SO:0000704"},{"id":"T1449","span":{"begin":756,"end":761},"obj":"SO:0005855"}],"attributes":[{"subj":"T1445","pred":"source","obj":"LitCovid-PMC-OGER-BB"},{"subj":"T1446","pred":"source","obj":"LitCovid-PMC-OGER-BB"},{"subj":"T1447","pred":"source","obj":"LitCovid-PMC-OGER-BB"},{"subj":"T1448","pred":"source","obj":"LitCovid-PMC-OGER-BB"},{"subj":"T1449","pred":"source","obj":"LitCovid-PMC-OGER-BB"}]},{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T139","span":{"begin":253,"end":256},"obj":"Disease"}],"attributes":[{"id":"A139","pred":"mondo_id","subj":"T139","obj":"http://purl.obolibrary.org/obo/MONDO_0018859"},{"subj":"T139","pred":"source","obj":"LitCovid-PD-MONDO"}]},{"project":"LitCovid-PD-CLO","denotations":[{"id":"T1120","span":{"begin":373,"end":378},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T1121","span":{"begin":594,"end":595},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T1122","span":{"begin":680,"end":685},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"}],"attributes":[{"subj":"T1120","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T1121","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T1122","pred":"source","obj":"LitCovid-PD-CLO"}]},{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T35821","span":{"begin":342,"end":345},"obj":"Chemical"}],"attributes":[{"id":"A14703","pred":"chebi_id","subj":"T35821","obj":"http://purl.obolibrary.org/obo/CHEBI_36751"},{"id":"A17168","pred":"chebi_id","subj":"T35821","obj":"http://purl.obolibrary.org/obo/CHEBI_62248"},{"subj":"T35821","pred":"source","obj":"LitCovid-PD-CHEBI"}]},{"project":"LitCovid-sentences","denotations":[{"id":"T372","span":{"begin":0,"end":70},"obj":"Sentence"},{"id":"T373","span":{"begin":71,"end":317},"obj":"Sentence"},{"id":"T374","span":{"begin":318,"end":465},"obj":"Sentence"},{"id":"T375","span":{"begin":466,"end":672},"obj":"Sentence"},{"id":"T376","span":{"begin":673,"end":793},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"attributes":[{"subj":"T372","pred":"source","obj":"LitCovid-sentences"},{"subj":"T373","pred":"source","obj":"LitCovid-sentences"},{"subj":"T374","pred":"source","obj":"LitCovid-sentences"},{"subj":"T375","pred":"source","obj":"LitCovid-sentences"},{"subj":"T376","pred":"source","obj":"LitCovid-sentences"}]},{"project":"LitCovid-PubTator","denotations":[{"id":"1457","span":{"begin":707,"end":714},"obj":"Species"}],"attributes":[{"id":"A1457","pred":"tao:has_database_id","subj":"1457","obj":"Tax:100569"},{"subj":"1457","pred":"source","obj":"LitCovid-PubTator"}],"namespaces":[{"prefix":"Tax","uri":"https://www.ncbi.nlm.nih.gov/taxonomy/"},{"prefix":"MESH","uri":"https://id.nlm.nih.gov/mesh/"},{"prefix":"Gene","uri":"https://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"CVCL","uri":"https://web.expasy.org/cellosaurus/CVCL_"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"LitCovid-PMC-OGER-BB","color":"#c693ec","default":true},{"id":"LitCovid-PD-MONDO","color":"#93ecac"},{"id":"LitCovid-PD-CLO","color":"#ec9394"},{"id":"LitCovid-PD-CHEBI","color":"#93aeec"},{"id":"LitCovid-sentences","color":"#c8ec93"},{"id":"LitCovid-PubTator","color":"#ec93e2"}]}]}}