User: sangram_keshari
sangram_keshari • 220
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- sangram_ksahu
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- 2 years, 8 months ago
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Bioinformatics Student, Working in the field of Computational Genomics.
Posts by sangram_keshari
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... Yes, you can plot a PCA on the normalized read-count or expression data of the transcriptome-assemblies. ...
written 4 weeks ago by
sangram_keshari • 220
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... For most of the annotation packages, we need to provide input keytype (such as ENSEMBL) to convert another keytype (ENTREZID).
Example:
library(AnnotationDbi)
library(org.Hs.eg.db)
input_ids <- c("ENSG00000121410", "ENSG00000175899", "ENSG00000256069", "ENSG00000171428")
...
written 11 weeks ago by
sangram_keshari • 220
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... Yes it will be logical, but it's just that fold change for few genes might be very less to be called as differentially expressed. ...
written 11 weeks ago by
sangram_keshari • 220
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... Hey thank you so much. It solved :) ...
written 11 weeks ago by
sangram_keshari • 220
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180
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... I have no problem with loading package if the `org_pkg` is a string, Problem comes with `mapIds()` ...
written 11 weeks ago by
sangram_keshari • 220
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... Thanks for the answer. Yes this gives an output.
But suppose I am receiving a string object in `org_pkg` (because its coming from an Rscript argument, and its always a string). Then how to convert that string object to an `AnnotationDbi` class. ...
written 11 weeks ago by
sangram_keshari • 220
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... I am trying to make the org.db (`x`) argument in `AnnotationDbi::mapIds()` as variable, But
genelist <- c("ENSG00000074800","ENSG00000116285","ENSG00000171603","ENSG00000049245")
org_pkg <- "org.Hs.eg.db"
library(AnnotationDbi)
library(org_pkg)
entrez_Ids <- mapIds( ...
written 11 weeks ago by
sangram_keshari • 220
• updated
11 weeks ago by
benformatics • 1.1k
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161
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... [Guangchuang Yu](https://www.biostars.org/u/3039/) Any known issue with newer version or R? ...
written 3 months ago by
sangram_keshari • 220
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1
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161
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... I am trying to run `clusterProfiler::enrichGO()` for 10 Human Ensemble IDs but its getting very slow. Sometimes it takes 15 minutes and other time more than half an hour. Also, its taking all the available RAM in a 8GB machine.
My R session dosn't have any other loaded package or objects.
I am usi ...
written 3 months ago by
sangram_keshari • 220
• updated
3 months ago by
jared.andrews07 • 3.4k
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... Tried to dig some more and I came up with this.
So there is some `libicui18n.so.54` library conflict. So I installed this:
conda install -c conda-forge icu=54.1
Not exactly sure if this is the solution. But its working for now.
...
written 4 months ago by
sangram_keshari • 220
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For Compare Microarray with RNA-Seq
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For A: Updated: Conference/Symposium/Seminar/Workshop alert 2018-2019
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For A: Updated: Conference/Symposium/Seminar/Workshop alert 2018-2019
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created an answer that has been accepted.
For A: cuffcompare: No novel genes found. Is this possible?
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