User: sangram_keshari
sangram_keshari • 180
- Reputation:
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- sangram_ksahu
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- 23 hours ago
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Bioinformatics Student, Working in the field of Computational Genomics.
Posts by sangram_keshari
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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 7 days ago by
sangram_keshari • 180
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... 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 ...
written 7 days ago by
sangram_keshari • 180
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... 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_keshari • 180
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... 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_keshari • 180
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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_keshari • 180
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... 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_keshari • 180
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... 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_keshari • 180
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5 follow
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... 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 ...
written 5 months ago by
sangram_keshari • 180
• updated
5 months ago by
johnsonnathant • 80
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... 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_keshari • 180
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... Yes, this pipeline is a better choice. ...
written 7 months ago by
sangram_keshari • 180
Latest awards to sangram_keshari
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5 days ago,
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For A: Updated: Conference/Symposium/Seminar/Workshop alert 2018-2019
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3 months ago,
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For A: Updated: Conference/Symposium/Seminar/Workshop alert 2018-2019
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12 months ago,
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For A: cuffcompare: No novel genes found. Is this possible?
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