User: arjuncsubra

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Posts by arjuncsubra

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Comment: C: How should I analyze the following dataset (GSE150847)?
... Yes - it was for training, thank you! ...
written 6 weeks ago by arjuncsubra0
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Comment: C: How should I analyze the following dataset (GSE150847)?
... To my understanding (I am really new to this), this dataset seems to have mouse genes in the rows and 6 columns which seem to be the test subjects. This dataset seems to involve mice that were gene-edited so they could become susceptible to the effects of COVID-19 respiratorily. I was just looking f ...
written 7 weeks ago by arjuncsubra0
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Comment: C: How should I analyze the following dataset (GSE150847)?
... I picked this dataset because I want to do some clustering related to COVID-19 and its effect on the lungs. ...
written 7 weeks ago by arjuncsubra0
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Comment: C: How should I analyze the following dataset (GSE150847)?
... I do not really have a particular hypothesis in mind; I would like to know what end product makes the most sense given this dataset and data type. ...
written 7 weeks ago by arjuncsubra0
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How should I analyze the following dataset (GSE150847)?
... Hi all, new to Bioconductor/scRNA-seq analyses here. For an upcoming project, I have chosen to analyze [this dataset][1], "Generation of a Broadly Useful Model for COVID-19 Pathogenesis, Vaccination, and Treatment". I have preprocessed and loaded the .tsv file (from supplemental files in GEO) int ...
R bioconductor rna-seq written 7 weeks ago by arjuncsubra0
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How to properly analyze following GEO DataSets
... Hi all, I am wondering whether my process for analyzing (and creating clustering maps) for the following two datasets is correct: [GSE150847][1] and [GSE145926][2]. I tried using getGEO but that does not seem to be correct as it is giving me 0 features for both accession values. **After looking a ...
geo R bioconductor rna-seq written 7 weeks ago by arjuncsubra0
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Comment: C: How to properly analyze many RDS files in Bioconductor
... It works, thank you so much! ...
written 8 weeks ago by arjuncsubra0
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Comment: C: How to properly analyze many RDS files in Bioconductor
... I have tried your command and it results in the following error message: Error: Matrices must have same number of columns in rbind2(argl[[i]], r) I also tried converting the first .rds object into a SingleCellExperiment using SingleCellExperiment(). I get the following error message: Erro ...
written 8 weeks ago by arjuncsubra0
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How to properly analyze many RDS files in Bioconductor
... **Link to the previous post for context:** https://www.biostars.org/p/450477/ Hi all, **I am analyzing a COVID-19 dataset (GSE150728) and my aim for this dataset is to create clustering maps.** For this dataset, I was instructed to download the RDS files present in the GSE150728_RAW.tar file from ...
R bioconductor rna-seq written 8 weeks ago by arjuncsubra0 • updated 8 weeks ago by benformatics1.9k
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0 Features for COVID-19 ExpressionSet through GEOQuery
... Hi all, Disclaimer: I am very new to Bioconductor. I am analyzing the GEO dataset "[GSE150728][1]" or " A single-cell atlas of the peripheral immune response to severe COVID-19". In doing this, I ran the getGEO command on this accession number. library(GEOquery) covid_data <- getGEO ...
R geoquery rna-seq written 9 weeks ago by arjuncsubra0 • updated 9 weeks ago by Kevin Blighe65k

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