User: kirannbishwa01

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Posts by kirannbishwa01

<prev • 199 results • page 1 of 20 • next >
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Comment: C: How to name the genome in karyoploteR ?
... It worked for lyrata the way you explained. Now, again it doesn't work for thaliana. > karyoploteR::plotKaryotype(genome = Athaliana) Error in is(genome, "GRanges") : object 'thaliana' not found I think the problem is with the naming, and I cannot find the right way. Why is there diffe ...
written 2 days ago by kirannbishwa01590
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Comment: C: Some clarification on enrichment analyses and pathway analyses?
... Hi Kevin, Can you tell me what tool was used to generate these plots and link to this plot, so I can check some description. Thanks, ...
written 3 days ago by kirannbishwa01590
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Comment: C: Some clarification on enrichment analyses and pathway analyses?
... Thank you so much Kevin for highlighting your points in such a comprehensive manner. It has cleared my doubts a lot. If I may have more questions, I will let you know. ...
written 5 days ago by kirannbishwa01590
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Some clarification on enrichment analyses and pathway analyses?
... I have analyzed my RNAseq data and identified the genes with significant `foldchanges and p-values`. **Next step is to do enrichment analyses.** I have been some extensive reading for last two weeks and have tried some analyses using command based tools, but things are getting confusing for me due ...
R gene enrichment pathview rna-seq bioinformatics written 8 days ago by kirannbishwa01590 • updated 7 days ago by Kevin Blighe6.7k
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Comment: C: karyoploteR: uncircle your genomes
... Can you please look into this question? https://www.biostars.org/p/281311/ https://support.bioconductor.org/p/102549/ ...
written 18 days ago by kirannbishwa01590
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How to name the genome in karyoploteR ?
... I really like the features that are provided in karyoploteR. https://bioconductor.org/packages/release/bioc/html/karyoploteR.html But, I am working with different organisms. I am able to find the organisms of interest using: available.genomes() My organisms of interest is Arabdidopsis lyrata ...
genome software error rna-seq karyoploter written 18 days ago by kirannbishwa01590 • updated 15 days ago by bernatgel840
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Comment: C: detecting allele specific expression of a gene at a specific locus without havin
... That sounds good that it is working. :) ...
written 9 weeks ago by kirannbishwa01590
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Comment: C: detecting allele specific expression of a gene at a specific locus without havin
... yeah, I have come across MBASED, but I think its for comparing ASE between two replicates of same sample. It may be otherwise, but I would look into the assumptions made by the tool/author in detail, before relying on ASE report. ...
written 9 weeks ago by kirannbishwa01590
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Answer: A: detecting allele specific expression of a gene at a specific locus without havin
... Check this software: https://www.nature.com/articles/srep21134 i.e GeneiASE, but I have not used it personally. The big deal in ASE analyses is that we are making assumptions that both the alleles have equal likelyhood of mapping, but the actual scenario is different (there is a mapping bias). So, ...
written 10 weeks ago by kirannbishwa01590
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Comment: C: How to plot coverage and depth statistics of a bam file
... I read all the answers/comments on this one. But, I have different opinion regarding this problem. `No matter how much deep sequencing you do (even in whole genome) there is a good probability that there will be good amount of genomic regions with 0 depth.` The reason is with short reads it is diffi ...
written 3 months ago by kirannbishwa01590

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