User: xie186

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xie1860
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Posts by xie186

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Comment: C: Individuals nested within blocks in DESeq2
... Thanks for your replying. 'ind' means indivudla. I have 8 individual animals in the experiment. I adapoted the code here: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#group-specific-condition-effects-individuals-nested-within-groups ...
written 14 months ago by xie1860
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Individuals nested within blocks in DESeq2
... Hi there, I'm trying to identfy the DEGs between treated samples and control samples. Here is the design: blk ind cnd ind.n Blk1 1 Ctrl 1 Blk1 1 Treated 1 Blk1 2 Ctrl 2 Blk1 2 Treated 2 Blk1 ...
deseq2 nested design written 14 months ago by xie1860 • updated 14 months ago by Michael Love25k
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ENSEMBL database for annotatr
... Hi Raymond, For Annotatr, it seems that it uses UCSC know genes as the database, right? Is there an easy way that I can use ENSEMBL database? The function read_regions will add one base on the left side of the coordinates, right? If the coordinate is 1 100 200, it will be 1 101 200 after reading u ...
annotatr written 20 months ago by xie1860 • updated 20 months ago by rcavalca130
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Comment: C: Unexpected results from annotatr
... Got it. Thanks for your help. I got a link for this gene (http://useast.ensembl.org/Mus_musculus/Gene/Summary?g=ENSMUSG00000025190;r=19:43499752-43524605).  It indeed has multiple transcripts with different TSS.  ...
written 20 months ago by xie1860
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Unexpected results from annotatr
... Hi Raymond @rcavalca, I was using R-3.4 and annotatr_1.4.0. I randomly checked one region (chr19 43510901 43511100). This region is assigned to two categories (1to5kb and introns) of the same gene (Got1). I don't understand how a region can be assigned to both 1to5kb and introns of the same ...
annotatr written 20 months ago by xie1860 • updated 20 months ago by rcavalca130
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Comment: C: 'fill_order' in annotatr
... Thanks.  ...
written 20 months ago by xie1860
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'fill_order' in annotatr
... Hi @rcavalca, I'm wondering that whether the parameter "fill_order" is just for the order of the legend? Or it will also be applied to priority information. For example, if there is a region that overlap with both CDS and UTR. The fill order is c("UTR", "CDS"). Will both of them be considered or jus ...
annotatr written 20 months ago by xie1860 • updated 20 months ago by rcavalca130
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Comment: C: How can I use Annotatr on CDS?
... Hi @rcavalca, I'm wondering that whether the parameter "fill_order" is just for the order of the legend? Or it will also be applied to priority information. For example, if there is a region that overlap with both CDS and UTR. The fill order is c("UTR", "CDS"). Will both of them be considered or jus ...
written 20 months ago by xie1860
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Comment: C: How can I use Annotatr on CDS?
...  I was using 'CDS' instead of 'cds', so it didn't work out. Thanks for developing such a nice package. ...
written 20 months ago by xie1860
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How can I use Annotatr on CDS?
... I'm using Annotatr on mm10. library(annotatr) #annots =c('mm10_cpg_islands', 'mm10_cpg_shores', 'mm10_cpg_shelves', 'mm10_cpg_inter') annots = c('mm10_genes_promoters', 'mm10_genes_5UTRs', 'mm10_genes_3UTRs', 'mm10_genes_exons', 'mm10_genes_introns', "mm10_genes_1to5kb", ' ...
exon cds utr annotatr written 20 months ago by xie1860 • updated 20 months ago by rcavalca130

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