User: Pin.Bioinf

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Pin.Bioinf60
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Malaga
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6 days, 14 hours ago
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1 year, 1 month ago
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Im a Health Engineering student doing an Artificial Intelligence master's degree and working on epigenetics

Posts by Pin.Bioinf

<prev • 53 results • page 1 of 6 • next >
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How to check for a variant (like *3) in public HepG2 cell line?
... Hello, I was requested to check for a specific gene *3 variant in public datasets in cell line HepG2. From my understanding, I believe I need to download .fastq files and check for that gene in IGV program visualizer or maybe dirrectly check if there are already variants for cell line HepG2 availa ...
hepg2 mutations variants written 11 days ago by Pin.Bioinf60
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Do all genes have a similar distributions of CpG sites across regions?
... Hello, I am wondering if all genes have a similar distribution of CpG sites, for example: the majority of the CpGs are in promoter, gene body... Little amoutn of cpgs at 5UTR and 3UTR,... Thank you ...
methylation written 24 days ago by Pin.Bioinf60 • updated 24 days ago by Devon Ryan81k
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Building a classifier model for sub tumours?
... Hello, I am wondering, If I have found that I have genes whose expression changes and CpGs whose methylation changes define sub groups of liver tumours, and I have big amounts of clinical data for patients of liver cancer, would that data be enough to try build a model that predicts response of ...
model software error rna-seq written 26 days ago by Pin.Bioinf60
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Correlations 5hmC 5mC Spearmann significance
... Hello, I have computed Spearmann correlations between 5mC beta values and expression values and also independently correlations between 5hmC (hydroxy) and expression. Is there higher chances for 5hmC to be significant, as same range changes - say 0.1 decrease in 5hmC and 0.1 decrease in 5mC are ...
rnaseq methylation written 4 weeks ago by Pin.Bioinf60
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Comment: C: expression and methylation integration
... That seems a very interesting idea! But i am not sure how I could do this. I have beta values for each CpG and for each sample (19 tumor, 19 peri-tumor). And I have the expression of each gene for the same samples. I would have to plot each pair cpg-gene (all the combinations) of the significant gen ...
written 4 weeks ago by Pin.Bioinf60
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expression and methylation integration
... Hello, I applied iClusterPlus to my data, in order to find the most significant driver cpgs and genes. I got two heatmaps: one for expression and one for methylation, and I got also the ids of the significant genes and cpgs, clearly distributed in 4 clusters. How could I establish if there is act ...
cluster omics integration R written 4 weeks ago by Pin.Bioinf60
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Comment: C: Help with heatmap
... This data was obtained by another bioinformatician who used to work for my colleague, and now she is asking I do some more analyses on it ...
written 5 weeks ago by Pin.Bioinf60
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Help with heatmap
... Hello, I want to check the heatmap for a number of genes but I am seeing all genes don't change through samples, ie. all genes have the same color across samples (I can only see color difference for the grouped genes). What I do is: I have RPKMS, this is a little part of the matrix: ...
R heatmap expression rpkm written 6 weeks ago by Pin.Bioinf60 • updated 6 weeks ago by Zhilong Jia1.3k
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Finding partially methylated domains starting from Illumina 450K IDAT files
... Hello, I have IDAT files from Illumina 450K, and I would like to find the PMDs (partially methylated domains) to further associate it to cpg density and tetranucleotide motifs. I know methpipe can do it (for .fastq files) is there a way to do it with minfi package or another? Thank you ...
metylation illumina450 R written 7 weeks ago by Pin.Bioinf60
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iClusterPlus no significant results
... Hello, Is anyone familiar with iClusterPlus? I have been trying to use iClusterPlus to integrate methylation and expression data I have, but It's not clear to me what I might be doing wrong: I am using beta values and RPKMS. 1) I filter out genes with low rpkm variability and probes (cpgs) with ...
omics methyl-seq rna-seq data integration written 8 weeks ago by Pin.Bioinf60

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