User: wuzefeng2008

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Posts by wuzefeng2008

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regioneR ignore the strand information when using the extendRegions() function
... Hi, there I am using the extendRegions function to get the extended GRanges, however, it automatically ignores the strand information.   For example:      > genes GRanges object with 33602 ranges and 1 metadata column: seqnames ranges strand | gene_id &l ...
regionr extendregions written 2 days ago by wuzefeng20080
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GenomicFeatures: How to extract a gene's upstream region of TSS up to the end position of the flanking (nearby) gene.
... Hi there, I wanted to extract the TSS up-stream region of each gene up to the end position (TTS) of the nearby gene. I only known the promoter function, but it seems can not deal with this problem. I could only get the GenomicRange object of  all genes from the gtf file by the following codes:   ...
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Netbiov vertex.color vector length error
... Hi, there, I am using Netbiov to visualize my  network (igrpah object).  When i was using the mst.plot function, the vertex.color parameter is a color vector, but it seems that it needs a vector with length is less than my vertex number. For example; gg<-make_ring(3) # make a 3-vertex netwo ...
visualization netowrk written 4 months ago by wuzefeng20080
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soggi average plot
... Hi, i have several bam files from chip-seq analysis, and  i want to plot the reads coverage around gene body. How to make normalization between samples to compare them and plot them in a same picture ? Thanks ...
cancer soggi multiple bam written 11 months ago by wuzefeng20080 • updated 11 months ago by kmezhoud10
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metagene error when plot metagene reads signal
... Hi, I am using ""metagene" to plot average reads signal around gene, but it gave error like this: Error in intoNbins(gr, bcount) : all 'width(gr)' must be >= 'n'. My command is : mg <- metagene$new(genes, "H3K4me3.bam", cores = 8, force_seqlevels = TRUE) After add the parameter of  "bin_ ...
metagene metagene$new written 12 months ago by wuzefeng20080 • updated 12 months ago by Charles Joly Beauparlant160
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Answer: A: ChIPpeakAnno binOverGene error
... Yes, if i set upstream.cutoff = 0, downstream.cutoff = 0, it works, but i wanted to show some flanking  regions.  and here was my sessioninfo: R version 3.4.2 (2017-09-28) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.04.5 LTS Matrix products: default BLAS: /usr/lib/openblas-ba ...
written 12 months ago by wuzefeng20080
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ChIPpeakAnno binOverGene error
... d<-binOverGene(cvglist,tr,upstream.cutoff =1000,downstream.cutoff = 1000)   ERROR: subscript contains out-of-bounds ranges ...
chippeakanno binovergene written 12 months ago by wuzefeng20080 • updated 12 months ago by Ou, Jianhong1.1k
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chipseeker annotation of focused genic regions
... I am attempting to annotate some ChIP-Seq data that I have called using MACS2. I just want to annotation peaks to specific regions, such as following classes : promoter, 5’ untranslated region (UTR), 3’ UTR, coding exon and intron),and intergenic regions from gtf file( convert to 'TxDB'). However,   ...
chipseeker annotatepeak written 13 months ago by wuzefeng20080 • updated 13 months ago by Guangchuang Yu1.1k

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