User: banerjeeshayantan

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Posts by banerjeeshayantan

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Effect of sample size on log fold change in gene expression analysis
... I am doing gene expression analysis using a set of 228 patients (52 positive and 176 negatives). I found a list of 17 DEGs that were significant (|log fold change| > 1 and p-value <0.1). I later found out that I can't include 30 patients from my negative class because they don't meet certain ...
R rna-seq written 12 weeks ago by banerjeeshayantan170 • updated 12 weeks ago by dsull1.5k
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Amino acid substitution to nucleotide substitution conversion
... I have a list of oncogenic mutations from the [OncoKB][1] database. The data looks someting like this Gene Alteration Oncogenicity CBL P417A likely oncogenic CBL N454D likely neutral I want to convert the above data set into the following format ...
R sequencing written 3 months ago by banerjeeshayantan170
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Similarity between DNA strings of two different classes
... I have a two sets of DNA strings of length 10 belonging to two different classes (class 1 and 2 say). A few examples from the dataset is given below: DNA_str_1 class ATTGGCGGCA 1 TAGGCGGGGC 2 ATTGCGCTGT 1 TAGGAGGAAG 2 Now, I want to construct a ...
similarity sequencing written 3 months ago by banerjeeshayantan170
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scRNA data for human muscle cells
... I have recently started learning scRNA seq data analysis and would want to apply my newly learned skills to a problem of my choice. I also have decent exposure to machine learning. I have learnt that sc-RNA-Seq is also quite valuable in cell-differentiation factor predictions (there are many papers ...
scrna machinelearning rna-seq written 4 months ago by banerjeeshayantan170
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Comment: C: How to download passenger mutations for cancer
... So basically play with the thresholds and pick the one that gives the best generalizable model. I am in fact worried about how all of this will play with the reviewers, but again like you said it is safe to build models on already publishes datasets. Thanks again for the links. ...
written 5 months ago by banerjeeshayantan170
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Comment: C: How to download passenger mutations for cancer
... I am mainly interested in coding region only (Substitution: missense, nonsense and coding silent). I am really confused regarding whether to use COSMIC as my primary source of data to build a model (Can you kindly go through the comment I made on @KevinBlighe's answer and let me know what you think? ...
written 5 months ago by banerjeeshayantan170
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Comment: C: How to download passenger mutations for cancer
... Many thanks for your detailed explanation. I am indeed using FATHMM-MKL and not FATHMM. Sorry for the confusion. I will definitely go through the papers you mentioned and try to get their data. But I was wondering whether to stick to COSMIC to construct the labels for my training set. It is a sizeab ...
written 5 months ago by banerjeeshayantan170
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How to download passenger mutations for cancer
... There exists a lot of literature on distinguishing driver mutations from passengers. I am trying to build my own deep learning model to do the same. I am facing some potential issues. First, I have downloaded COSMIC mutation data and used the FATHMM labels to designate drivers (positive examples) in ...
passenger mutations driver mutations cancer written 5 months ago by banerjeeshayantan170 • updated 5 months ago by Collin840
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Unable to understand the input to the tablemaker tool
... I have two sequenced RNA seq samples (bam files generated using minimap2). My goal is prepare the input for the ballgown tool in order to perform gene expression analysis. The following are the commands that I used. First, for each sample, I assembled the RNA seq segments using StringTie and then ...
software error rna-seq written 5 months ago by banerjeeshayantan170
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Common bioinformatics tools required to analyze the mutational distribution in mice genomes
... I have 21 normal-tumour matched whole-genome sequencing data from isogenic mice samples. I intend to perform the following: 1. Distribution of substitutions, indels, rearrangements and copy number changes across samples. 2. Mutational signature analysis of the samples. I am aware of tools su ...
genome next-gen written 7 months ago by banerjeeshayantan170

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Popular Question 10 weeks ago, created a question with more than 1,000 views. For Finding driver genes from a cancer dataset
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