User: Researcher

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Researcher30
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Posts by Researcher

<prev • 32 results • page 1 of 4 • next >
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Comment: C: GO enrichment analysis from peaks to corresponding genes for each MSigDB Oncogen
... Hi @jared.andrews07 Thank you for your kind help, this is really helpful. I am just curious to ask about "GO" termID as you specified in the above example. How can I get the similar for any other pathway of my interest like for example "Sonic Hedgehog (Shh) Pathway". ...
written 4 days ago by Researcher30
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Comment: C: GO enrichment analysis from peaks to corresponding genes for each MSigDB Oncogen
... Hi @jared.andrews07 I have a list of annotated chip-seq peaks and their corresponding genes. In order to check if there is any enrichment for the genes that are from any specific oncogenic or any immunological pathway, I have used rGREAT. rGREAT with its getEnrichmentTables() provided me a file wit ...
written 5 days ago by Researcher30
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GO enrichment analysis from peaks to corresponding genes for each MSigDB Oncogenic Signatures or GO IDs using rGREAT
... Hi All, I used rGREAT to do GO enrichment analysis for the peak calls from macs2, where I got enriched GO IDs and MSigDB Oncogenic Signatures. Can anyone help me to automate this process in such a way that I will get a table with all enriched GO IDs or MSigDB Oncogenic Signatures with corresponding ...
genes chip-seq rgreat msigdb oncogenic signatures written 6 days ago by Researcher30 • updated 4 days ago by jared.andrews072.5k
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Comment: A: Question about ChromHMM overlap enrichment
... Hi @nanoide, Even I am trying to do something similar. Was just curious to ask were you able to get the answers what you were looking for? I'll appreciate if you can share your experience here and the strategy you followed to get this done. Thanks ...
written 7 days ago by Researcher30
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Comment: A: ChromHMM: chromatin states to genome % coverage?
... Hi @Sy80, Even I am looking for answer to my similar question. Was just curious to ask were you able to get it done. I'll appreciate if you can share your experience here and the strategy you followed to get this done. Thanks ...
written 7 days ago by Researcher30
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Comment: A: ChromHMM - annotation of chromatin states
... Hi @Julia, did you get the answer to your question? I am also facing similar problem. If you figured out your answers please share here too. Thanks ...
written 7 days ago by Researcher30
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Comment: C: Predicting survival of cancer patients using glmnet cox
... Hi @Kevin, Thank you for your reply and a nice explanation. Yes I am using TCGA data and need some more clarification for your comments. > Researchers do not typically use survival data in this way. What do you suggest then, how should I use the survival data of patients to predict their surviv ...
written 8 days ago by Researcher30
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Answer: A: ChromHMM 15 State Descriptions (Genic Enhancer)
... Can we generate consensus plots from multiple samples of each subtype using Chromhmm? ...
written 12 days ago by Researcher30
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Answer: A: How to calculate the AUC value for a ranger RF model ?
... Hi debitboro, By any chance, did you get this answer? ...
written 25 days ago by Researcher30
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Comment: C: Correct approach to identify differential binding in samples (with no duplicates
... @ATpoint, I am looking forward to your kind suggestion. Thanks ...
written 6 weeks ago by Researcher30

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