User: Martombo

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Martombo2.0k
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Posts by Martombo

<prev • 254 results • page 1 of 26 • next >
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Answer: C: Percentage of RNA-seq reads in exonic, intronic, intergenic and splice junction
... You can use read_distribution.py from RSeQC for this. It works with a bed format as input. ...
written 8 days ago by Martombo2.0k
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Answer: A: Mutation in one gene in TCGA data
... cBioPortal is most likely the easiest choice indeed. Cancers are classified by tissue of origin, so you'll find colorectal cancer under the "Bowel" section. Frameshift mutations are also typically included in the report. ...
written 26 days ago by Martombo2.0k
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Comment: C: Gene Co-expression analysis with less number of replicates
... I think the critical point here is not (only) the number of replicates, but rather the number of different condition / samples you have. Given that the original poster only had 3 different samples, I guess it was impossible in his case to build a gene co-expression network. With so few samples in fa ...
written 27 days ago by Martombo2.0k
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Comment: C: Why DE genes are not among highly variable genes between groups
... did you determine your "highly variable genes" as it is indicated in your first reference? If so, these are not highly variable genes between groups A and B, as you call them, but rather genes with the highest variance in your data. That means they can change a lot independently of the group. For th ...
written 6 weeks ago by Martombo2.0k
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Comment: C: Selection of hub gene on the basis of node degree
... I think the hub concept applies especially well to a protein-protein interaction network, where you have "sticky" proteins, ubiquitins, plymerases, histones, GNGs that are in some cases associated to a lot of other proteins. A co-expression network doesn't necessarily have hubs. 40 connections in pa ...
written 8 weeks ago by Martombo2.0k
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Comment: C: Normalization and differential analysis in ATAC-seq data
... I believe you could use [diffBind][1] strategy: merge the peaks of different samples, count the number of reads in it and perform a differential analysis on those counts. I don't however have experience on ATAC-seq myself, so I cannot guarantee that's the best approach. [1]: https://bioconductor ...
written 9 weeks ago by Martombo2.0k
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Comment: C: project of MutsigCV/ MuSic
... indeed it's not! ...
written 12 weeks ago by Martombo2.0k
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Answer: A: project of MutsigCV/ MuSic
... On MutSigCV's [page][1] on GenePattern you can find a link to the [publication][2] where it was first introduced, which is not open-access unfortunately. MuSiC's [one][3] is, however. [1]: http://software.broadinstitute.org/cancer/software/genepattern/modules/docs/MutSigCV [2]: https://www.nat ...
written 12 weeks ago by Martombo2.0k
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Comment: C: pythonic equivalent to reduce() in R GRanges - how to collapse ranged data?
... in what structure is your data stored in python? ...
written 3 months ago by Martombo2.0k
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Answer: A: Identifying enriched pathways that overlap among a range of databases
... You could definitely retrieve the gene lists associated with every geneset and compute the overlap between them, but I'm not sure that can help you much. I think what people normally do is to use comprehensive genesets, like the ones present in [MSigDB][1]. An algorithm that I know is taking direct ...
written 3 months ago by Martombo2.0k

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Scholar 4 months ago, created an answer that has been accepted. For C: what is tAKR in the last of htseq results.
Scholar 4 months ago, created an answer that has been accepted. For C: what is tAKR in the last of htseq results.
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: microRNA transcription start site prediction
Scholar 5 months ago, created an answer that has been accepted. For C: what is tAKR in the last of htseq results.
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Teacher 6 months ago, created an answer with at least 3 up-votes. For A: microRNA transcription start site prediction
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Scholar 2.4 years ago, created an answer that has been accepted. For C: what is tAKR in the last of htseq results.
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Scholar 2.6 years ago, created an answer that has been accepted. For C: what is tAKR in the last of htseq results.
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