User: kamula

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kamula10
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Location:
NYU
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8 months, 4 weeks ago
Joined:
7 years, 5 months ago
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Posts by kamula

<prev • 8 results • page 1 of 1 • next >
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Tool to determine percentage of transcripts that have the intron cleaved from RNA-seq data
... I'm interested in analyzing the splicing of a transcript that has two exons. Is there a tool that will provide the percentage of transcripts that have the intron removed, vs. transcripts with the intron still present? I'd imaging it would quantify the percentage of reads that either span the intro ...
rna-seq written 9 months ago by kamula10
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Comment: C: How to do per gene scaling before clustering?
... I guess my question might boil down to: I know z-scoring is a good idea, but how to avoid amplifying the signal of noisy genes? ...
written 13 months ago by kamula10
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How to do per gene scaling before clustering?
... I'd like to cluster genes that are co-expressed from my dataset (6000 genes X 300 conditions) I'd like a scaling method that does not amplify noisy measurements, but still brings genes with similar gene expression profiles (but different dynamic ranges) together. Here's an example, everything is in ...
R scaling rna-seq clustering normalization written 13 months ago by kamula10 • updated 11 months ago by Biostar ♦♦ 20
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Paper enrichment based on gene list
... About a year ago I stumbled upon a website that allowed one to supply a query list of gene names, and it would return papers that were enriched for those gene names. It may or may not have also worked with keywords. I'm having a lot of trouble finding it and was wondering if anyone could point me ...
gene written 21 months ago by kamula10 • updated 21 months ago by Jean-Karim Heriche17k
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Determine if two RNA-seq samples are repeats of each other
... I have 13 RNA-seq samples, all from the same condition, but with slight variations in genotype (that i believe are functionally insignificant in this condition). How can I convince myself that I can use these 13 samples as replicates? I've thought of using DE-Seq2 to find that there are no DE gene ...
rna-seq written 2.6 years ago by kamula10 • updated 2.5 years ago by Biostar ♦♦ 20
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Comment: C: Merging microarray datasets
... this looks really cool, thanks! ...
written 2.9 years ago by kamula10
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Merging microarray datasets
... I'd like to get my hands on a microarray dataset with as many conditions as possible. One thought that I had was to simply concatenate many individual microarray datasets together, however it seems that they often dont have the same probes, and sometimes are in different units (fold change, intensit ...
geo microarray written 2.9 years ago by kamula10 • updated 2.9 years ago by Jean-Karim Heriche17k
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Finding the TFs that regulate a set of genes
... I've Identified a list of co-expressed genes, and I'd like to figure out what is regulating their expression. Currently what I have done is run this group of genes through scope to identify motifs in their promoters. How do I then take those motifs and associate them with a TF? Or is there a better ...
expression motif tf written 3.2 years ago by kamula10 • updated 2.2 years ago by jin80

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Popular Question 21 months ago, created a question with more than 1,000 views. For Finding the TFs that regulate a set of genes

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