User: 9606

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9606320
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Posts by 9606

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5
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325
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Triplet frequencies in human genome
... Hello, does anybody know if it exists a list of nucleotide triplets associated with their frequency in the human genome (hg19 or grch38 are both ok) ? Of course I can count it by myself, but I just wish to save some time. ...
genome counts written 11 months ago by 9606320 • updated 11 months ago by finswimmer13k
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1
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366
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Simulated background and peak smoothing in MACS2
... I cite from the Wiki page of the Encode Imputation Challenge: > We use the MACSv2 peak caller to compute the fold-enrichment and statistical significance of smoothed counts (150 bp smoothing window) of read-starts (5' ends of reads) at each position in the genome relative to the expected number ...
background macs2 peakcalling written 12 months ago by 9606320 • updated 12 months ago by ATpoint34k
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Clarification on GDC Methylation data
... I need to work with methylation data. GDC provides a vast dataset of methylation-array samples. I noticed that for all the probes, they associate one or more ENSEMBL transcript ID. My (most probably stupid) question is: are these data a sort of "Whole Exome Sequencing" rather than a "Whole Genom ...
dataset tcga methylation gdc written 22 months ago by 9606320
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Venue to publish a bioinformatics tool
... I would like to (try to) publish a software I have been developing; the software is for analyzing and integrating data from ENCODE, and of course will be open source. I know about Bioinformatics APPLICATIONS NOTES as a possible venue, but I would like to evaluate alternatives. Can anyone point me ...
publication software academy bioinformatics written 23 months ago by 9606320 • updated 23 months ago by EagleEye6.6k
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Understanding cBioPortal data
... I have some problem understanding the data from cBioPortal. For example, refer to the cell line [HCC1428][1]. For this cell line TP53 is reported as **DeepDeleted**, but its mRNA z-score is 0.79 (then, it is overexpressed). ![enter image description here][2] Isn't this contradictory? What am I mi ...
mrna cna cbioportal cnv data written 2.1 years ago by 9606320
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TCGA data, relationship between different sources
... I am to analyze TCGA data for RNA-Seq of many tumors. I found that data can be downloaded either from Genomic Data Commons: https://gdc-portal.nci.nih.gov/ or from UCSC Xena: https://xenabrowser.net/datapages/?host=https://tcga.xenahubs.net For what it concerns RNA-Seq data, they do have some di ...
tcga data-sources rna-seq written 3.2 years ago by 9606320 • updated 3.2 years ago by genomax83k
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Web service (possible REST) for GO enrichment
... I have to to test the enrichment for several (tens of) gene clusters. I know there exist many web application for doing such analysis. I would like use some web service in order to automatically perform the enrichment, in order to speed up the procedure. I found some similar question on BioStarts ...
enrichment gene ontology web services written 3.5 years ago by 9606320 • updated 3.5 years ago by Alex30
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Comment: C: Measure the correlation between genes
... Exactly. Pearson can only capture linear relationships. Mutual information criteria could be a better choice, I was wondering if some particular criterion has been adopted in the literature. ...
written 3.5 years ago by 9606320
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Measure the correlation between genes
... Given a set of genes, and some hundreds of experiments in different conditions (from TCGA), I want to measure the pairwise correlation of expression of any pair of genes. So far, I have been using the Pearson correlation, but this measure has some well known limitations. Also, it may be hard to int ...
gene expression rna-seq written 3.5 years ago by 9606320
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NGS throughput historical data
... Hi all, I am writing a review on NGS sequencing. I found data about the cost per sequenced megabase, made publicly available by NHGRI. ![enter image description here][1] [1]: https://www.genome.gov/images/content/costpergenome2015_4.jpg I was wondering if similar reliable and updated data ex ...
next-gen sequencing written 3.9 years ago by 9606320 • updated 3.9 years ago by harold.smith.tarheel4.5k

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Popular Question 11 months ago, created a question with more than 1,000 views. For Software for drawing peak shapes
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