User: banerjeeshayantan
banerjeeshayantan • 170
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Posts by banerjeeshayantan
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... 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 ...
written 12 weeks ago by
banerjeeshayantan • 170
• updated
12 weeks ago by
dsull • 1.5k
1
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... 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
...
written 3 months ago by
banerjeeshayantan • 170
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... 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 ...
written 3 months ago by
banerjeeshayantan • 170
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... 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 ...
written 4 months ago by
banerjeeshayantan • 170
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... 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
banerjeeshayantan • 170
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... 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
banerjeeshayantan • 170
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177
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... 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
banerjeeshayantan • 170
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6 follow
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... 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 ...
written 5 months ago by
banerjeeshayantan • 170
• updated
5 months ago by
Collin • 840
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... 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 ...
written 5 months ago by
banerjeeshayantan • 170
0
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141
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... 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 ...
written 7 months ago by
banerjeeshayantan • 170
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