User: mahejabeen.nidhi

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New User
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4 days, 22 hours ago
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1 month, 2 weeks ago
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Posts by mahejabeen.nidhi

<prev • 10 results • page 1 of 1 • next >
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load failed for EGSEA on R Studio
... I am trying to install EGSEA however, I keep getting the following error Error: package or namespace load failed for ‘EGSEA’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called ‘mnormt’ I tried to install mnormt which resulted in ...
egsea rna-seq rstudio written 5 days ago by mahejabeen.nidhi10
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Heatmap outputs unusual plot
... I am not sure where I am making the error #sort by log2FC sortedbyLFC <- DESeq2resultsSTARalignment.tabular[order(-DESeq2resultsSTARalignment.tabular$log2.FC.), ] #create dataframe sorteddataframe <- data.frame(sortedbyLFC, row.names = "GeneID") first5000genes <- h ...
deseq2 rna-seq heatmap written 16 days ago by mahejabeen.nidhi10 • updated 16 days ago by RamRS27k
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Comment: C: DESeq DataSet from HTSeqCount Error
... I made the edits, and still am getting an error > #make directory with htseq-counts > directory <- "/Users/mahejabeennidhi/Documents/DrKwan/rnaseq6samples/htseqcounts" > sampleFiles <- grep("count",list.files(directory), value = TRUE) > sampleCondition <- c("IL4 ...
written 17 days ago by mahejabeen.nidhi10
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DESeq DataSet from HTSeqCount Error
... As my lab does not a lot of computational power, I had used Galaxy for alignment and HTSeq. To produce better graphs for downstream analysis, I had to switch to RStudio. I am using the six samples from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132732 There are two treatment conditions ...
htseq galaxy rna-seq written 17 days ago by mahejabeen.nidhi10
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Comment: C: GSEA expression dataset error update
... I was just reading about why not to use excel! I am running the GUI of GSEA on my macbook. I will let you know if it works out this time. Thank you so much! ...
written 23 days ago by mahejabeen.nidhi10
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Comment: C: GSEA expression dataset error update
... Thank you, Kevin I created the file on excel and saved it as tab delimited text so I would assume it to be just like your layout. I also did put a # where I wrote hashtag. ...
written 24 days ago by mahejabeen.nidhi10
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GSEA expression dataset error update
... I created the expression dataset using the normalised counts from DESeq2. First few rows are as follows hashtag1.2 60668 6 NAME description R848rep1 R848rep2 R848rep3 noRNArep1 noRNArep2 noRNArep3 ENSG00000000005 NA 0 0 0 0 0 0 ENSG00000000419 NA 1.1724063 ...
de rna-seq gsea written 24 days ago by mahejabeen.nidhi10 • updated 24 days ago by Kevin Blighe61k
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Comment: C: Setting up environment for RNASeq on university HPCC CondaHTTPError: HTTP 000 CO
... Very fair point. I already emailed the admin. Hopefully he can resolve this issue. Thank you! ...
written 6 weeks ago by mahejabeen.nidhi10
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Comment: C: Setting up environment for RNASeq on university HPCC CondaHTTPError: HTTP 000 CO
... That is an amazing idea! I think I will try to do that. I am new to working with HPCC. Do you have a git repo on building containers like that or other HPCC functions? Thank you again! ...
written 6 weeks ago by mahejabeen.nidhi10
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Setting up environment for RNASeq on university HPCC CondaHTTPError: HTTP 000 CONNECTION FAILED
... $ conda install -c bioconda fastqc Collecting package metadata (current_repodata.json): failed CondaHTTPError: HTTP 000 CONNECTION FAILED for url Elapsed: - An HTTP error occurred when trying to retrieve this URL. HTTP errors are often intermittent, and a simple re ...
hpc connection conda rna-seq http written 6 weeks ago by mahejabeen.nidhi10

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