User: marco

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marco10
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Posts by marco

<prev • 15 results • page 1 of 2 • next >
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Filter out transcription factors from a list of genes
... Hello! I have a list of genes (DEGs, from an RNA-seq analysis) and I would like to filter out from this list only those genes coding for known transcription factors (human). I wondered if there is any web tool or R package which can accomplish such a function, which can be way more straightforward ...
transcription factors rna-seq written 13 days ago by marco10
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Comment: C: Pathways Network Analysis Cytoscape
... Thanks so much! It was very helpful :) ...
written 13 days ago by marco10
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Pathways Network Analysis Cytoscape
... Hello! I am new to the network analysis and, following the suggestions of some colleagues, I am using Cytoscape to perform it. I have some RNA-seq data (list of UP and DOWN DEGs) which I first used to generate on STRING a scoring file (.txt file) to use as input into Cytoscape. Together with it, I ...
pathways network cytoscape rna-seq written 21 days ago by marco10 • updated 19 days ago by scooter330
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Comment: C: GSEA analysis error
... I am pretty new to this, so I am not sure to understand exactly what you mean. I have uploaded my expression dataset where I have one column with all the gene symbols and other columns with the normalized counts for each sample. ...
written 4 weeks ago by marco10
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GSEA analysis error
... Hello! I am trying to run GSEA on my RNA-seq dataset using the tool provided by the Broad Institute, which I have downloaded from their webpage. I am using as input files my expression dataset (including all the genes, not only DEGs) Gene Symbols as identifiers, followed by the normalized counts fo ...
gsea rna-seq written 4 weeks ago by marco10 • updated 29 days ago by Danielle B10
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Comment: C: SICER for ChIP-seq broad peaks
... Thanks a lot! I will then use epic2 instead. You are right when you say "Be aware that bamCoverage only visualizes the sequencing data, it does not call any peaks." I am aware of it but I did not mention it in my post. I usually always use bamCompare normalizing the ChIP sample against its input. ...
written 9 weeks ago by marco10
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SICER for ChIP-seq broad peaks
... Hello! I am trying for the first time to run SICER for calling broad peaks in my ChIP-seq dataset. Many people suggested me to use this tool rather than MACS2 (with --broad option). When running SICER, I am calling it with ```recognicer``` command, since it seems to be the correct one for broad pe ...
chip-seq sicer written 9 weeks ago by marco10
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Comment: C: Samtools problem with running (Conda)
... Works for me as well after running ```conda remove samtools```. MacOS Catalina v10.15.3 ...
written 10 weeks ago by marco10
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Comment: C: GSEA analysis RNA-seq data
... Thanks a lot! I will do so then. I was including only the DEGs with a log2FC threshold of > 0.5 for UP DEGs and < -0.5 for DOWN DEGs. Including all the genes means that I also have to remove the adjusted pvalue threshold? I have tried this way and some pathways now pass the FDR threshold and ...
written 12 weeks ago by marco10
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Comment: C: GSEA analysis RNA-seq data
... I am running GSEA through the WebGestalt website, where it asks me to report a list of two columns: one should contain the gene identifier and another one the associated "scores", which I assume are the log2FC values of the retrieved DEGs. I do upload together both the UP and DOWN DEGs. Is there ...
written 12 weeks ago by marco10

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