User: up201505092

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Posts by up201505092

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Comment: C: GDC TCGA LUAD dataset iCluster.group parameter
... Hi @igor and thank you for your answer! The classification in the iCluster link doesn't match the classification I have downloading through TCGABiolinks. Mine is identical to the classification provided in the 'Supplementary Data' section of the LUAD paper I referenced. I've also browsed Xena and ...
written 7 weeks ago by up2015050920
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Comment: A: GDC TCGA LUAD dataset iCluster.group parameter
... Hi Kevin, The classification is provided in the luad paper in the supplementary data section and on the lusc paper not. I'm not sure if it was forgotten by lapse, because the same methodology was applied and the paper also references performing integrative clustering, the figures showing the iClust ...
written 7 weeks ago by up2015050920
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GDC TCGA LUAD dataset iCluster.group parameter
... Hi, I downloaded TCGA data using R TCGABiolinks framework. The LUAD clinical dataset has a variable`paper_iCluster.group`, I've found this resource [TCGA_Marker_Papers][1], which says that all the variables starting by `paper_` come from PanCancerAtlas publications. I've tracked down the origin of ...
tcgabiolinks R icluster tcga dataset written 7 weeks ago by up2015050920 • updated 7 weeks ago by igor12k
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TCGA LUAD clinical dataset iCluster.group variable
... Hi, I'm conducting research using TCGA lung cancer datasets. In the LUAD clinical dataset, there is a variable called `paper_iCluster.group` which I can't find the definition for anywhere on [TCGA metadata documentation][1] This variable takes integer values from [1, 6] and has missing values fr ...
dataset tcga variable clinical written 8 weeks ago by up2015050920
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Survival analysis using CoxPH - Effect of covariates
... Hi and sorry for the long post in advance, I'm doing a survival analysis of lung cancer patients using Python's lifelines package. According to the documentation, the function plot_partial_effects_on_outcome() plots the effect of a covariate on the observer's survival. I do understand that the CoxP ...
survival cox-ph written 8 weeks ago by up2015050920

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