User: Thind Amarinder
Thind Amarinder • 30
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Posts by Thind Amarinder
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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 Amarinder • 30
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... 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 Amarinder • 30
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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 Amarinder • 30
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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 Amarinder • 30
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... **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 ...
written 15 days ago by
Thind Amarinder • 30
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... 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 ...
written 23 days ago by
Thind Amarinder • 30
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... 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 Amarinder • 30
• updated
4 weeks ago by
Kevin Blighe ♦ 63k
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... Better. contact to author and ask for clarification. sometimes researcher make mistakes at the time of submission. ...
written 6 weeks ago by
Thind Amarinder • 30
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... 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 Amarinder • 30
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... [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 Amarinder • 30
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