User: ZZzzzzhong

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ZZzzzzhong210
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1 year, 10 months ago
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z***********@zju.edu.cn

Posts by ZZzzzzhong

<prev • 10 results • page 1 of 1 • next >
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Comment: C: How to input data for DESeq2 from individual HTSeq count?
... Just like the variable condition sampleFiles <- c('cowan1','cowan2','cowan3','isolate1','isolate2','isolate3') remember sampleFiles correspond with condition ...
written 19 months ago by ZZzzzzhong210
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Answer: A: How to input data for DESeq2 from individual HTSeq count?
... directory <- "/path/to/your/files/" directory is where your htseq-count output files are located. sampleFiles <- grep("Bacteria",list.files(directory),value=TRUE) samplesFiles is a variable which points to your htseq-count output files, condition <- c('Bacteria1','Bacteria1',' ...
written 19 months ago by ZZzzzzhong210
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Answer: A: 2 peak files in plotAvgProf2 [ChIPseeker]
... files <- list(peak2,peak3) promoter <- getPromoters(TxDb=txdb, upstream=3000, downstream=3000) tagMatrixList <- lapply(files, getTagMatrix, windows=promoter) plotAvgProf(tagMatrixList, xlim=c(-3000, 3000)) ...
written 19 months ago by ZZzzzzhong210
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Answer: A: How to get strand information in the bed file of macs1.4 peak calling output?
... Transcriptome usually comes from fixed chains.peak_result is your MACS out put and genes.gtf is your annotation file. intersectBed -wo -a peak_result -b genes.gtf | awk -v OFS="\t" '{print $1,$2,$3,"*","*",$10}'|uniq > Peaks.bed fastaFromBed -s -f genome.fa -bed Peaks.bed -fo Peaks.fa ...
written 19 months ago by ZZzzzzhong210
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Answer: A: The m6A-Seq analysis
... It's not very exactly to apply s standard Chip-Seq analysis pipeline to m6A-Seq analysis.RNA' expression is dynamic.So the distribution model is different with chipseq'data(exomePeak is designed to call peaks of m6A seq).m6Aseq belong to RNA which involves the splicing site, it's best to use RNA ali ...
written 19 months ago by ZZzzzzhong210
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Comment: C: Is it possible to visualize ChIP peaks of three different samples in one plot us
... if you want to label 1_peak as name1(Any name you want) you can do that`files <- list(name1=1_peak,name2=2_peak,name3=3_peak)` ...
written 19 months ago by ZZzzzzhong210
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Answer: A: Is it possible to visualize ChIP peaks of three different samples in one plot us
... This is easy to implement by CHIPseeker. Let's say 1_peak,2_peak and 3_peak are your peak_file. files <- list(1_peak,2_peak,3_peak) peakAnnoList <- lapply(files, annotatePeak, TxDb=txdb,tssRegion=c(-3000, 3000), verbose=FALSE) plotDistToTSS(peakAnnoList) + theme(plot.title = eleme ...
written 19 months ago by ZZzzzzhong210
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Answer: A: Data Sorting R
... You can define a new column: df$3 = df$1 * df$2 then df <- subset(df, df$3 < 0, select = 1:2) ...
written 19 months ago by ZZzzzzhong210 • updated 19 months ago by zx87549.2k
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Answer: A: Can be merged biological replicates?
... > For the experiment with several replicates, it is recommended to > concatenate several ChIP-seq treatment files into a single file. To do > this, under Unix/Mac or Cygwin (for windows OS), type: `$ cat replicate1.bed replicate2.bed replicate3.bed > all_replicates.bed` For BAM or SAM ...
written 20 months ago by ZZzzzzhong210 • updated 20 months ago by ATpoint34k
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Answer: A: Best method to do clustering (sub-group) single cell RNA-Seq data?
... you can try Seurat(https://satijalab.org/seurat/pbmc3k_tutorial.html).it only need the genecount matrix,then you could do clustering ,DE,and so on ...
written 22 months ago by ZZzzzzhong210

Latest awards to ZZzzzzhong

Appreciated 16 months ago, created a post with more than 5 votes. For A: Data Sorting R
Appreciated 17 months ago, created a post with more than 5 votes. For A: Data Sorting R
Scholar 17 months ago, created an answer that has been accepted. For A: Data Sorting R
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Is it possible to visualize ChIP peaks of three different samples in one plot us
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: 2 peak files in plotAvgProf2 [ChIPseeker]
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Is it possible to visualize ChIP peaks of three different samples in one plot us
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Is it possible to visualize ChIP peaks of three different samples in one plot us

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