User: c_u

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c_u160
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Posts by c_u

<prev • 107 results • page 1 of 11 • next >
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Comment: C: Regarding Split reads and discordant reads
... Wait, then what's the difference between a Split Read and a discordant read of the first kind (large genomic distance between the read pairs). They appear the same from this explanation ...
written 17 days ago by c_u160
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Comment: C: Suggestion needed for finding fusion transcripts
... thanks for the comment and for STAR-fusion ...
written 17 days ago by c_u160
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Suggestion needed for finding fusion transcripts
... Hi, I have RNA-Seq data coming from human tissue samples, and I am interested in finding fusion transcripts specific to the disease case. There are a bunch of software out there that report fusion transcripts and I have come across the following two reviews (by the same group) that compare the diff ...
fusion-transcripts rna-seq written 17 days ago by c_u160
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Answer: A: What were the most impactful Bioinformatics papers published this year
... I believe Deep Learning continued to lead the way in many subfields of biology, One obvious winner was Alphafold that Mensur mentioned. I would like to offer three more notable contributions - Deep Learning to identify kinase inhibitors - https://www.nature.com/articles/s41587-019-0224-x Deep Lea ...
written 5 weeks ago by c_u160
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Forum: What were the most impactful Bioinformatics papers published this year
... 2019 is coming to a close, so I thought of asking this question - what were some of the Bioinformatics papers published this year that you thought were the most impactful. Preprints count. I am not looking for papers that got the most number of citations (which would be a poor metric for papers pu ...
bioinformatics forum written 5 weeks ago by c_u160
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Comment: C: Program to find genes up/down-regulated by a given gene
... Hey hugo, yes! And we are planning to publish it early next year. Will upload a preprint soon and will post the link here ...
written 5 weeks ago by c_u160
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Comment: C: tximport output should be integer values, IS NOT.
... Thanks a lot Ram. I think I may have misunderstood. I think it is true that the job of tximport is to provide count values to DESeq2 (which need to be integer) but I guess it doesn't do it on its own (using the tximport function). Rather I think that conversion to integer happens using DESeqDataSetF ...
written 6 weeks ago by c_u160
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Comment: C: tximport output should be integer values, IS NOT.
... Ram, I changed my code to have DESeqDataSetFromTximport() instead of DESeqDataSetFromMatrix(), and it worked fine. Thanks a lot! ...
written 6 weeks ago by c_u160
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Comment: C: tximport output should be integer values, IS NOT.
... Hi Ram, I understood that this is one of the main functions of `tximport` from here - https://www.biostars.org/p/143458/#144003 ...
written 6 weeks ago by c_u160
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Answer: A: name of the figure
... To me it looks like overlapping horizontal violin plots, that have been smoothed at the edges. This could be a design that Guardant360 came up with (the legend mentions that the figures were generated by Guardant360). [Here][1] is an example of a horizontal violin plot. You can read more about violi ...
written 6 weeks ago by c_u160

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Centurion 6 weeks ago, created 100 posts.
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Program to find genes up/down-regulated by a given gene
Popular Question 3 months ago, created a question with more than 1,000 views. For Program to find genes up/down-regulated by a given gene
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Popular Question 16 months ago, created a question with more than 1,000 views. For Doing GSEA analysis on a set of genes
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