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 • 56 results • page 1 of 6 • next >
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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 7 days ago by sangram_keshari180
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DESeq2 Error while loading from a conda Environment
... I am trying to run `DESeq2` from a conda environment. Installation was successful with all the dependencies as per conda, but while loading the library I came up with this error. > library(DESeq2) Loading required package: S4Vectors Loading required package: stats4 Loading requ ...
deseq2 conda written 7 days ago by sangram_keshari180
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Comment: C: What is the accurate order of preprocessing steps in DNA Microarray gene express
... some packages like `gcrma` take care of normalization and log transformation. You can refer here- http://www.bioconductor.org/packages/release/bioc/html/gcrma.html Then you can use these value to perform DE analysis using `limma` ...
written 11 days ago by sangram_keshari180
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Comment: C: How to subset ExpressionSet based on vector of sample names
... Once you get the ExpressionSet in a data frame object you can try to perform `subset()` a base function or `filter()` from dplyr package. ...
written 11 days ago by sangram_keshari180
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Answer: A: How to work with Deepvariant
... **Deepvariant on local system:** This is a link to nf-core pipeline to run on a local system with enough resources: https://github.com/nf-core/deepvariant ...
written 13 days ago by sangram_keshari180
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Comment: C: Compare SE and PE gene expression data.
... Here is a PCA plot: https://imgur.com/a/sv6zEw8 Towards extreme left the PE datasets and towards extreme right SE. ...
written 5 months ago by sangram_keshari180
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Comment: C: Compare SE and PE gene expression data.
... After normalization also, The scaling in both the datasets is different, which is not comparable. Note: I want to compare relative expression. ...
written 5 months ago by sangram_keshari180
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Compare SE and PE gene expression data.
... I want to compare the gene expression of similar tissue-type coming from one SE and another PE dataset (each having 3 biological replicates in both). And also both are from different labs with different protocols. So I tried to normalize both the datasets with `normTransform` in DESeq2 package fro ...
deseq2 rna-seq written 5 months ago by sangram_keshari180 • updated 5 months ago by johnsonnathant80
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Comment: C: May I use numreads for doing DGE after quantifying by Salmon
... Yes, but also it has few functions for a seamless integration with few outputs from other packages: According to that Bioconductor vignettes link shared by @WouterDeCoster: > the tximport pipeline offers the following benefits: (i) this approach corrects for potential changes in gene length acr ...
written 7 months ago by sangram_keshari180
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Comment: C: May I use numreads for doing DGE after quantifying by Salmon
... Yes, this pipeline is a better choice. ...
written 7 months ago by sangram_keshari180

Latest awards to sangram_keshari

Teacher 5 days ago, created an answer with at least 3 up-votes. For A: Updated: Conference/Symposium/Seminar/Workshop alert 2018-2019
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Updated: Conference/Symposium/Seminar/Workshop alert 2018-2019
Scholar 12 months ago, created an answer that has been accepted. For A: cuffcompare: No novel genes found. Is this possible?
Supporter 16 months ago, voted at least 25 times.
Autobiographer 18 months ago, has more than 80 characters in the information field of the user's profile.

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