User: sangram_keshari
sangram_keshari • 250
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- https://sksahu.net/
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Bioinformatics and Computational Genomics.
Posts by sangram_keshari
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... From this above data seems like you already have othergroup in your data. That above code tried to add group based on conditions.
The above code will generate a dataframe something like this -
mydf
Entrez group othergroup
gene1 upregulated A
gene2 downregulated A
gene3 upreg ...
written 9 months ago by
sangram_keshari • 250
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... Found a file in KEGG website - https://www.genome.jp/kegg-bin/download_htext?htext=br08610&format=htext&filedir= (I am surprised why this is not available in [their standard rest API](http://rest.kegg.jp/).)
Anyways, Here is a rough solution around the downloaded file `br08610.keg` using th ...
written 10 months ago by
sangram_keshari • 250
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... Suppose I have a KEGG organism code and wants to check the corresponding NCBI organism Taxonomic ID.
I am able to find [this online tool available from KEGG](https://www.genome.jp/kegg/tool/map_taxonomy.html).
Also, http://rest.kegg.jp/list/organism only returns the list of KEGG organisms with tax ...
written 10 months ago by
sangram_keshari • 250
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... In R you can simply Principal Components Analysis
```
pca <- prcomp(read_count_df)
```
For plotting
```
library(ggfortify)
autoplot(pca, loadings.label = TRUE)
``` ...
written 12 months ago by
sangram_keshari • 250
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Comment:
C: help kegg pathway
... Input data - https://pathview.uncc.edu/overview#input
You need some additional information to view input gene on the pathway graph ...
written 14 months ago by
sangram_keshari • 250
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... Here is an explanation from DESeq2 vignettes - [Count data transformations](http://www.bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#count-data-transformations)
...
written 15 months ago by
sangram_keshari • 250
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... First of all, DESeq2 does not do read counting. The main purpose of it to do differential analysis using the RAW read counts generated from tools like FeatureCount.
Although DESeq2 internally transform the RAW read count value to do the analysis. I guess that's what you getting confused with read c ...
written 15 months ago by
sangram_keshari • 250
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... Yes, you can plot a PCA on the normalized read-count or expression data of the transcriptome-assemblies. ...
written 17 months ago by
sangram_keshari • 250
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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 19 months ago by
sangram_keshari • 250
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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 19 months ago by
sangram_keshari • 250
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For RNA-Seq reads maped against DNA or cDNA??
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For A: cuffcompare: No novel genes found. Is this possible?
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