User: sangram_keshari

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IISER Mohali
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Bioinformatics and Computational Genomics.

Posts by sangram_keshari

<prev • 72 results • page 1 of 8 • next >
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Comment: C: compareProfiler - Assistance on how I can modify codes for different states
... 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 11 weeks ago by sangram_keshari230
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Answer: A: KEGG organism ID to NCBI taxonomy ID mapping API
... 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 3 months ago by sangram_keshari230
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KEGG organism ID to NCBI taxonomy ID mapping API
... 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 ...
kegg written 3 months ago by sangram_keshari230
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Comment: C: PCA for multiple transcriptome-assemblies
... In R you can simply Principal Components Analysis ``` pca <- prcomp(read_count_df) ``` For plotting ``` library(ggfortify) autoplot(pca, loadings.label = TRUE) ``` ...
written 5 months ago by sangram_keshari230
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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 7 months ago by sangram_keshari230
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Comment: C: deseq2 read counts vs featurecount read counts
... 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 8 months ago by sangram_keshari230
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Answer: C: deseq2 read counts vs featurecount read counts
... 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 8 months ago by sangram_keshari230
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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 10 months ago by sangram_keshari230
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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 12 months ago by sangram_keshari230
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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 12 months ago by sangram_keshari230

Latest awards to sangram_keshari

Popular Question 8 months ago, created a question with more than 1,000 views. For RNA-Seq reads maped against DNA or cDNA??
Popular Question 9 months ago, created a question with more than 1,000 views. For RNA-Seq reads maped against DNA or cDNA??
Voter 10 months ago, voted more than 100 times.
Popular Question 10 months ago, created a question with more than 1,000 views. For Compare Microarray with RNA-Seq
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Updated: Conference/Symposium/Seminar/Workshop alert 2018-2019
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Updated: Conference/Symposium/Seminar/Workshop alert 2018-2019
Scholar 2.2 years ago, created an answer that has been accepted. For A: cuffcompare: No novel genes found. Is this possible?
Supporter 2.6 years ago, voted at least 25 times.
Autobiographer 2.6 years ago, has more than 80 characters in the information field of the user's profile.

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