User: teabonng

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teabonng20
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Posts by teabonng

<prev • 29 results • page 1 of 3 • next >
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Comment: C: Connectivity Map dataset
... Hi ATpoint, I have edited the question. Basically, i cannot download the raw .cel files of the rankMatrix.txt, a connection cannot be established. I have tried multiple ways of downloading but still nothing works. The problem seems to be on their server side. Thanks ...
written 5 days ago by teabonng20
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Connectivity Map dataset
... Hi Everyone, Is anybody else having trouble with accessing the Connectivity Map dataset from https://portals.broadinstitute.org/cmap/? I have registered an account and whenever I try to download the .cel files or the rankMatrix.txt, it never works. Is there anywhere else where the raw dataset is de ...
dataset connectivity map written 5 days ago by teabonng20
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Construction of coexpression networks from multiple datasets
... Hi Everyone, I plan to construct coexpression networks to find modules using various independent datasets from databases such as GEO. Would it be valid that for each dataset, I calculate the fold changes of all genes with respect to untreated samples. Then I combine all the multiple datasets to cal ...
coexpression networks coexpression written 4 months ago by teabonng20
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Node degree-weighted graph
... Hi everyone, I would like to ask for suggestions as how to convert a weighted graph from an unweighted graph, with the weights based on the degrees of nodes in the edges. Also, if there is a good python package for this that can handle thousands of nodes. Thank you very much! ...
network biology written 5 months ago by teabonng20
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ChIP-Seq tag counts
... Hi Everyone, Can I use tag counts from ChIP-Seq data as inputs for machine learning? I did not call peaks, however, so that the features will not be simply binary. Thank you for your help. teabonng ...
chip-seq machine learning written 11 months ago by teabonng20 • updated 11 months ago by WouterDeCoster42k
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Histone modification patterns
... Hi Everyone, Can anyone refer me to a good reference that shows evidence that genes that belong to the same regulatory pathway have similar histone modification patterns that can be statistically analyzed? Thank you. ...
chromatin pattern written 12 months ago by teabonng20
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PPI networks in disease vs. healthy
... Hi Everyone, I was reading about some PPIs recently. Please excuse if my question is too simple. My question is, if i reconstruct PPIs from healthy and diseased individuals from omics data, would you expect that the reconstructed PPIs will be different, even if only a few nodes? ...
ppi networks written 12 months ago by teabonng20 • updated 12 months ago by Kevin Blighe53k
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Comment: C: Machine learning predictor has no correlation with output variable
... Hi Jean-Karim, Thank you for your help. I would just like to further clarify, since the logistic regression takes into account the individual contributions of each feature, but I did not add any interaction terms. In this case, I'm not sure if i can say that there is some interaction among the fea ...
written 14 months ago by teabonng20
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Machine learning predictor has no correlation with output variable
... Hi Everyone, I built a logistic regression classifier for predicting genes that has around 75% accuracy. Predictor A is a transcription factor that is a top predictor. However, when I look at the the scatterplot there is absolutely no correlation and the positive and negative examples show the same ...
machine learning written 14 months ago by teabonng20 • updated 14 months ago by Jean-Karim Heriche21k
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Comment: C: Neural networks feature importance
... Hi karl.stamm, Can you provide an example on how to adapt Garson's algorithm for multiple neurons? Can I calculate the importances with respect to each neuron instead? Thanks ...
written 15 months ago by teabonng20

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Popular Question 5 months ago, created a question with more than 1,000 views. For edgeR - normalized counts from multiple datasets
Popular Question 9 months ago, created a question with more than 1,000 views. For edger model matrix design of linear model

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