User: Thind Amarinder

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30
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Frankfurt
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https://www.researchga...
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57 minutes ago
Joined:
5 years, 4 months ago
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Posts by Thind Amarinder

<prev • 49 results • page 1 of 5 • next >
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Answer: A: PHYLIP to MEGA converter
... [https://www.biostars.org/p/173079/#454867][1] I answered it here. [1]: https://www.biostars.org/p/173079/#454867 ...
written 2 days ago by Thind Amarinder30
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Answer: A: error in file conversion with mega software
... Using R, it is very simple, Here is my R script. [https://github.com/amarinderthind/phlyip-distance-to-Mega-distance/blob/master/distane_matrix_conversion.r][1] library(readr) dist1 <- read_table2("input_file_phylip_distance.txt", col_names = FALSE, skip = 1) names1 <- dist ...
written 2 days ago by Thind Amarinder30
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Comment: C: Meta Analysis on RNA-seq data
... There are various approaches to do that; however, I would suggest you go for Ranks based methods, such as robust rank aggregation. [https://www.pnas.org/content/107/33/14621][1] This article may answer your other questions as well. It all depends on the biological experiments. [1]: https://www.p ...
written 11 days ago by Thind Amarinder30
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Comment: C: ceRNA network identification
... It all depends on the biological interpretation of the network. If your network is not so big, you may want to include all the interactions. On the other hand, if the network is too big, you may wish only to consider overlapping interactions. Sometimes you can also use the threshold based on interac ...
written 11 days ago by Thind Amarinder30
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Tutorial: RNASeq tutorial for gene differential expression analysis
... **RNA-seq-tutorial-for-gene-differential-expression-analysis** This tutorial is based on Bioconductor packages, RNAseq gene differential expression analysis, including filtering, preprocessing, visualization, clustering, and Enrichment. In case you have any queries or questions, please feel free t ...
tutorial transcriptomics rna-seq written 15 days ago by Thind Amarinder30
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query regarding miRNA-mRNA co-expression analysis
... I am trying to integrate expression data of miRNA-mRNA (~20 samples). I have a few queries such as **which one is the best method for co-expression calculation (my interest is anticorrelation) 'Pearson', 'spearman','Kendall', 'Mutual information' etc? and why?** My aim is to extract miRNA-mRNA pai ...
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Answer: A: Biomart Bioconductor - Retrieving All Entrezgenes Of Hsapiens_Gene_Ensembl
... Nowadays it is like "entrezgene_id" library(biomaRt) mart <- useMart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl") genes=getBM(attributes = c("hgnc_symbol", "entrezgene_id"), filters = "hgnc_symbol", values = all, bmHeader = TRUE, mart = mart) ...
written 4 weeks ago by Thind Amarinder30 • updated 4 weeks ago by Kevin Blighe63k
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Comment: C: How to get fastq files for individual replicates?
... Better. contact to author and ask for clarification. sometimes researcher make mistakes at the time of submission. ...
written 6 weeks ago by Thind Amarinder30
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Comment: C: Having trouble running ANNOVAR annotator for the first time please help!
... Check if the file "hg19_refGene.txt" exists or not. if yes, you can specify the path of the file manually. ...
written 6 weeks ago by Thind Amarinder30
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Answer: A: How to process raw data (.cel files) from GEO and get annotation of genes
... [Geo2R][1] is the simplest option. After defining the groups in an online tool you can also download the R script for local use. For some platform, you may need to download the probes annotation file platform commercial website (Affymetrix or others). [https://www.biostars.org/p/96508/#443952][2] ...
written 6 weeks ago by Thind Amarinder30

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Popular Question 4.3 years ago, created a question with more than 1,000 views. For Not able to retrieve PDB id from standalone blast against PDB

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