User: elb

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elb170
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Torino
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Posts by elb

<prev • 79 results • page 1 of 8 • next >
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Comment: C: Chip-seq best practice data analysis
... no of course.....there's not perfection but at least improvements... ...
written 19 days ago by elb170
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Comment: C: Chip-seq best practice data analysis
... Really really thank you very much!!!! Incredibly helpful for me. I'm reading some papers on tools tailored for Chip-exo and I found this: http://chipexo.sourceforge.net. It seems that with Chip-exo the background noise will be "solved". I can compare with known Chip-seq derived data like for example ...
written 20 days ago by elb170
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Comment: C: Chip-seq best practice data analysis
... Hi. I have to analize Chip-exo data for nascent RNAs but I'm totally new to the Chip analysis (I perform RNA seq analysis) and so my idea was to practice a little bit. ...
written 21 days ago by elb170
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Chip-seq best practice data analysis
... Hi guys, is here a complete and gold standard/best practice on-line tutorial (with tools and commands) I could follow in order to have a template on how to computationally analyse methylation/ acetylation/PolII/CTCF Chip-seq data from Next-seq 500 NGS? I mean from alignment on human to downstream an ...
chip-seq written 21 days ago by elb170 • updated 20 days ago by ATpoint25k
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segmentation of Chip-exo DATA
... Hi guys, I would like to ask you if there is a computational tool to segment ChIP-exo data or if the segmentation is the same as that used for canonical ChIP-seq data ...
chip-seq written 27 days ago by elb170 • updated 27 days ago by genomax74k
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Comment: C: Variability explained by a core of genes
... Do you think it could be a statistically efficient approach? I will create it soon! ...
written 10 weeks ago by elb170
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Comment: C: Variability explained by a core of genes
... Yes I understand the point. My idea...what about to prioritize genes according to the frequency of high loadings across PCs? Suppose you select top 13 PCs according to elbow (or horn depending on what you desire). Suppose, also, to categorise the loadings in bins (ranges of values. This could be byp ...
written 10 weeks ago by elb170
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Comment: C: Variability explained by a core of genes
... Can I ask you the rationale behind the "offset <- (max(x[, i]) - min(x[, i])) * rangeRetain" cutoff choice that appears in the code? My point is that it gives many genes with loadings around 0 that I expect not to contribute to the explained variance. Why they are retained? Also using a 1% cut of ...
written 10 weeks ago by elb170
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Comment: C: Variability explained by a core of genes
... I agree with you about the optimal threshold! ...
written 11 weeks ago by elb170
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Comment: C: Variability explained by a core of genes
... Dear Kevin, thank you very much for your precious help and suggestions. I tried to use PCAtools and I have to say that I like it a lot and I will support it. The unbiased selection of the PCs is very helpful for my purposes. I have just one question. plotloadings force users to select the rangeRetai ...
written 11 weeks ago by elb170

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Popular Question 5 weeks ago, created a question with more than 1,000 views. For regulatory regions discovery and alignment
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Great Question 18 months ago, created a question with more than 5,000 views. For Check For Co-Expressed Genes In Microarray Experiments
Popular Question 20 months ago, created a question with more than 1,000 views. For regulatory regions discovery and alignment
Popular Question 20 months ago, created a question with more than 1,000 views. For Transcription Factors Annotation
Great Question 4.6 years ago, created a question with more than 5,000 views. For Check For Co-Expressed Genes In Microarray Experiments
Popular Question 4.6 years ago, created a question with more than 1,000 views. For Transcription Factors Annotation
Student 4.6 years ago, asked a question with at least 3 up-votes. For Looking For Network Visualization Tools
Popular Question 6.9 years ago, created a question with more than 1,000 views. For Check For Co-Expressed Genes In Microarray Experiments
Popular Question 6.9 years ago, created a question with more than 1,000 views. For Fold Change Detection In Affymetrix Microarray Data Without Replicates
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