User: liux.bio
liux.bio • 10
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Posts by liux.bio
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... Hi,
Biostars. I have a time course RNA-seq experiments(7 time points) with two replicates and I want to cluster genes using Mfuzz package. Following the reference and the posts in Biostar, I filter the genes using SD(standard deviation). But I think it's not enough and I want to care about the bio ...
written 13 months ago by
liux.bio • 10
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... Hello, have your paper been published? If so, could you give me a link? I want to gain the TFs list. Thanks!
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written 14 months ago by
liux.bio • 10
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... Got it. Thank you!
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written 16 months ago by
liux.bio • 10
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... Hi,
Biostars. I have a list of genes with Ensembl gene ids and I want to filter out non-coding genes and get protein-coding genes. I am using Bioconductor package BiomaRt, but can't find a direct way. Any suggestions?
Many thanks!
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written 16 months ago by
liux.bio • 10
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... How about total non-overlapping introns per gene lengths? Introns are grouped by transcripts.How could I group them by genes? Thanks!
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written 20 months ago by
liux.bio • 10
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... Yes,I tried. I read the help but I can't understand it. For a GRangesList split by transcripts, it deletes all the overlapping between the transcripts and in the transcripts,right?
I will read the help carefully.Thanks!
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written 21 months ago by
liux.bio • 10
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... Hello,biostars.
I am using bioconductor to get sequences of introns, UTRS, flanking regions for genes. I have a set of genes, I want gene-centered sequences of introns, UTRS, flanking regions. I am using packages such as Biostrings, GenomicFeatures. I gain sequences of UTRS, flanking regions, intron ...
written 21 months ago by
liux.bio • 10
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... Thanks.GATHER is a good tool, I will try it.
I can't open http://cdwscience.blogspot.com/2013/03/bioinformatics-101-gene-expression.html. Could send me again or send me a text?
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written 21 months ago by
liux.bio • 10
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... Hello,
Biostars. I want to look for over-represented transcription factor binding sites for a given set of genes. I have learned a lot from similar questions in Biostar and papers. But I still have a problem and can't find the precise answer. According to papers, the promoter region contains 5'UTR, ...
written 21 months ago by
liux.bio • 10
• updated 21 months ago by
Charles Warden ♦ 3.8k
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... Thanks.It makes use of DAVID and Bingo separately.
...
written 22 months ago by
liux.bio • 10
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