User: zjhzwang

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zjhzwang180
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Posts by zjhzwang

<prev • 53 results • page 1 of 6 • next >
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Comment: C: Using limma to find differentially methylated probes across clusters
... Have you tried [chAmp][1]? [1]: https://www.bioconductor.org/packages/release/bioc/html/ChAMP.html ...
written 20 months ago by zjhzwang180
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Comment: C: parse data in excel or using perl
... Please give a more clear example, your description is hard to understand. ...
written 20 months ago by zjhzwang180
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Comment: C: Merge two data sets
... You can read CSV files into R separately, and use the gene IDs as rownames of data frame, then you can use `cbind` to merge two data frame. ...
written 20 months ago by zjhzwang180
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Comment: C: Translate from hsa-let- to MIMAT type
... You can find what you want from miRbase[Download site][1] [1]: ftp://mirbase.org/pub/mirbase/CURRENT/miRNA.xls.gz ...
written 20 months ago by zjhzwang180
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Comment: C: Translate from hsa-let- to MIMAT type
... From your data, **hsa-let-7a-5p** is miRNA' s ID, and it has serval stem-loop *hsa-let-7a-1 hsa-let-7a-2 hsa-let-7a-3*. So you need translate you data to stem-loop then map to MIMAT type. ...
written 21 months ago by zjhzwang180
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Comment: C: Gene list from bed file
... You can use **biomaRt** package to get the genes' chromesome information, then you can map your bed file to gene symbols or gene IDs. ...
written 21 months ago by zjhzwang180
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Comment: C: DE analysis of single cell RNAseq
... Maybe you can use DESeq2 with your ReadCounts. ...
written 21 months ago by zjhzwang180
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Comment: C: RNA-seq batch effect correction
... If you want to remove batch effect, maybe this package will be helpful. [sva][1] [1]: https://www.bioconductor.org/packages/release/bioc/html/sva.html ...
written 21 months ago by zjhzwang180
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Comment: C: Gene Body methylation
... So does it means that methylation can cause not only negative effect but also positive effect? ...
written 21 months ago by zjhzwang180
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Comment: C: Annotation of ChIP-seq peaks after MACS
... Maybe you can use this package [ChIPpeakAnno][1] [1]: https://bioconductor.org/packages/release/bioc/html/ChIPpeakAnno.html ...
written 22 months ago by zjhzwang180

Latest awards to zjhzwang

Scholar 23 months ago, created an answer that has been accepted. For A: statistical tests to show the specificity of a phenomenon (eg increase in H3K27m
Scholar 23 months ago, created an answer that has been accepted. For A: statistical tests to show the specificity of a phenomenon (eg increase in H3K27m
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: statistical tests to show the specificity of a phenomenon (eg increase in H3K27m

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