User: banerjeeshayantan

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Posts by banerjeeshayantan

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Comment: C: Pathway analysis of a list of possible cancer driver genes
... Thanks for your answer. I will do an intersection with the said papers and look for overlaps. In the third paper that you linked with your answer, the authors first identified 460 genes and then showed that these genes cluster into known cancer-related pathways. I am looking for something like this. ...
written 9 weeks ago by banerjeeshayantan190
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Pathway analysis of a list of possible cancer driver genes
... I have a list of 130 genes that were predicted as drivers using my own prediction algorithm. Is there any systematic way to analyze this list of genes to see whether they affect known "oncogenic" pathways? I ran this through the STRING database and downloaded the list of KEGG and REACTOME pathways t ...
driver genes pathway analysis cancer written 9 weeks ago by banerjeeshayantan190 • updated 9 weeks ago by Kevin Blighe71k
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Include gene ontology codes in the plots generated using the enrochplot package
... I was trying to plot the gene ontology (BP; CC; MF) terms for a set of genes as shown in the figure below. The codes used to generate the plot is `go <- enrichGO(de, OrgDb = "org.Hs.eg.db", ont="all") dotplot(go, split="ONTOLOGY") + facet_grid(ONTOLOGY~., scale="free")` However, instead ...
enrichplot gsea functional enrichment analysis written 10 weeks ago by banerjeeshayantan190 • updated 10 weeks ago by ATpoint46k
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Types of base substitutions
... I was reading this Wikipedia article on Mutational Signatures and I came across this section titled **Types of mutations: base substitutions**. I don't understand why the C>A mutations are indistinguishable from G>T. When we are cataloging the mutations we do have the strand information, righ ...
genome snp written 3 months ago by banerjeeshayantan190
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How to run bedtools from inside a python program
... I have been using the bedtools to extract fasta sequences based on genomic positions mentioned in a bed file. The command that I usually use os the following: bedtools getfasta -fi input.fa -bed input.bed -fo out.fa Now I want to implement the same command line from a python program. This i ...
bedtools python commandline written 4 months ago by banerjeeshayantan190 • updated 4 months ago by Joe19k
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Comment: C: Batch effect removal with the help of sva
... Thanks a lot for your help and for providing the links. It's just that I have gone through quite a few papers that have adjusted for batch effects using Combat and used the corrected data for finding DEGs. But after learning about the apparent perils of going down that road, I am pretty sure I won't ...
written 4 months ago by banerjeeshayantan190
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Comment: C: Batch effect removal with the help of sva
... Understood. So basically I wanted to see the before and after plots and check how one can use sva to discover the unwanted variations in your data. However, for obtaining the batch corrected data, I am using Combat and obtaining the cleaned expression matrix outputted by the same. Hope that's ok. ...
written 4 months ago by banerjeeshayantan190
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Comment: C: Batch effect removal with the help of sva
... Thanks a lot for your explanation. The concept is more clear to me now. Basically, find the set of covariates that best explains the variability in the dataset due to batch effect and produce a boxplot of the inferred covariate (sv[,2]) in this case vs the actual effect. Could you also please let me ...
written 4 months ago by banerjeeshayantan190
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Batch effect removal with the help of sva
... I was recently going through the concepts required to remove batch effects from gene expression data. In particular, I was going through [this tutorial][1] by Jeff Leek and trying out the codes mentioned there. From what I have understood from the analysis, SVA is similar to PCA and tries to find tw ...
sva gene expression batch effect written 4 months ago by banerjeeshayantan190 • updated 4 months ago by Papyrus690
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Feature extraction pipeline for CHASMplus
... I am trying to extract the features that were used to train the CHASMplus tool for driver mutation prioritization. Although the list of features is available in the [Supplementary Materials][1], I was wondering if there was a way to extract features for a new set of mutations (Chromosome/Position/Re ...
chasmplus written 5 months ago by banerjeeshayantan190

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