User: sangram_keshari

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sangram_ksahu
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Bioinformatics Student, Working in the field of Computational Genomics.

Posts by sangram_keshari

<prev • 65 results • page 1 of 7 • next >
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Comment: C: PCA for multiple transcriptome-assemblies
... Yes, you can plot a PCA on the normalized read-count or expression data of the transcriptome-assemblies. ...
written 4 weeks ago by sangram_keshari220
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Auto find keytype from input keys (list of IDs)
... 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") ...
gene R written 11 weeks ago by sangram_keshari220
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Comment: C: Gene set enrichment analysis with logFC and PValue
... 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_keshari220
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Comment: C: Make org.db dynamic in AnnotationDbi::mapIds()
... Hey thank you so much. It solved :) ...
written 11 weeks ago by sangram_keshari220
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Comment: C: Make org.db dynamic in AnnotationDbi::mapIds()
... I have no problem with loading package if the `org_pkg` is a string, Problem comes with `mapIds()` ...
written 11 weeks ago by sangram_keshari220
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Comment: C: Make org.db dynamic in AnnotationDbi::mapIds()
... 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_keshari220
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Make org.db dynamic in AnnotationDbi::mapIds()
... 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( ...
R bioconductor written 11 weeks ago by sangram_keshari220 • updated 11 weeks ago by benformatics1.1k
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Comment: C: clusterProfiler::enrichGO() is getting very slow
... [Guangchuang Yu](https://www.biostars.org/u/3039/) Any known issue with newer version or R? ...
written 3 months ago by sangram_keshari220
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clusterProfiler::enrichGO() is getting very slow
... 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 ...
R clusterprofiler go written 3 months ago by sangram_keshari220 • updated 3 months ago by jared.andrews073.4k
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Answer: A: DESeq2 Error while loading from a conda Environment
... 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_keshari220

Latest awards to sangram_keshari

Voter 20 days ago, voted more than 100 times.
Popular Question 29 days ago, created a question with more than 1,000 views. For Compare Microarray with RNA-Seq
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Updated: Conference/Symposium/Seminar/Workshop alert 2018-2019
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Updated: Conference/Symposium/Seminar/Workshop alert 2018-2019
Scholar 16 months ago, created an answer that has been accepted. For A: cuffcompare: No novel genes found. Is this possible?
Supporter 21 months ago, voted at least 25 times.
Autobiographer 22 months ago, has more than 80 characters in the information field of the user's profile.

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