User: ZZzzzzhong

gravatar for ZZzzzzhong
ZZzzzzhong200
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12 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 9 months ago by ZZzzzzhong200
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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 9 months ago by ZZzzzzhong200
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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 9 months ago by ZZzzzzhong200
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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 9 months ago by ZZzzzzhong200
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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 9 months ago by ZZzzzzhong200
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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 9 months ago by ZZzzzzhong200
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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 9 months ago by ZZzzzzhong200
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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$3 < 0, select = 1:2) ...
written 9 months ago by ZZzzzzhong200 • updated 9 months ago by zx87547.8k
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Answer: A: Can be merged biological replicates?
... > For the experiment with several replicates, it is recommended to > concatenate several ChIP-seq treatment files into a single file. To do > this, under Unix/Mac or Cygwin (for windows OS), type: `$ cat replicate1.bed replicate2.bed replicate3.bed > all_replicates.bed` For BAM or SAM ...
written 9 months ago by ZZzzzzhong200 • updated 9 months ago by ATpoint19k
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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 12 months ago by ZZzzzzhong200

Latest awards to ZZzzzzhong

Appreciated 5 months ago, created a post with more than 5 votes. For A: Data Sorting R
Appreciated 7 months ago, created a post with more than 5 votes. For A: Data Sorting R
Scholar 7 months ago, created an answer that has been accepted. For A: Data Sorting R
Teacher 7 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 7 months ago, created an answer with at least 3 up-votes. For A: 2 peak files in plotAvgProf2 [ChIPseeker]
Teacher 8 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 9 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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