User: massimofaggiani

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Posts by massimofaggiani

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Comment: C: Quantification of acetylation enriched regions at transcription factor binding s
... Thank you for your answer, but I managed to do that simply by adding `-c` (count) option in `bedtools window` command. Now I would like to filter only the regions for which there is an increase in acetylation peaks in the TF knock-out with respect to wild-type, having two separate bed files. Any sug ...
written 5 weeks ago by massimofaggiani0
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Quantification of acetylation enriched regions at transcription factor binding sites (WT vs KO)
... I am still at the beginning of ChIP-seq data analysis and am stuck in the following problem: I want to quantify the enriched peaks of H3K27ac at the proximity (5kb) of each binding site of a transcription factor under study, and make a comparison with the knock-out of the same TF. I have already cal ...
chip-seq written 6 weeks ago by massimofaggiani0 • updated 6 weeks ago by Prakash2.0k
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Comment: C: How do I load a peak file in ChIPseeker?
... How do I create such path to my bed files? I just replaced the example files with my bed file in GEO_sample_data folder. ...
written 6 months ago by massimofaggiani0
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Comment: C: How do I load a peak file in ChIPseeker?
... Thank you, but I already found that page. It's not clear to me how the five files are found and loaded in R. ...
written 6 months ago by massimofaggiani0
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How do I load a peak file in ChIPseeker?
... I am new to ChIPseq data analysis and am wondering how is the syntax for loading a bed file in R package chipseeker; so far I just used sample data provided with the package. For example, if I write: peak <- readPeakFile("file.bed") An error occurs since it cannot open the connection and find s ...
chipseeker written 6 months ago by massimofaggiani0 • updated 5 months ago by mossysuffi0
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Comment: C: trying to reproduce heat map made via cBioportal using download data
... Thanks. So is it essentially hierarchical clustering to find the maximum number of similarities and cluster them together? Because in my case, I have clustered only 4 genes and perhaps it's quite expected to not observe any clustering. ...
written 13 months ago by massimofaggiani0
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Comment: C: trying to reproduce heat map made via cBioportal using download data
... What is the basis of heatmap clustering? From what factor depends the order of patients after selecting "cluster heatmap" in the oncoprint? Thank you. ...
written 13 months ago by massimofaggiani0
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Obtain a gene expression matrix from TCGA in R
... Hello everyone, I am quite new to bioinformatics, currently learning TCGA analysis in R. So far I worked with few genes at the time using the cgdsr package, but how would I proceed if I need to retrieve a full gene expression matrix from TCGA colorectal cancer cohort? ...
R tcga rna-seq written 16 months ago by massimofaggiani0 • updated 16 months ago by ATpoint41k

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