User: kanwarjag

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kanwarjag1.0k
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Posts by kanwarjag

<prev • 360 results • page 1 of 36 • next >
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RNA-seq and histone modifictaion
... If I have an RNA-seq data of control and treated samples. Can I estimate changes in H3K4me3, H3K27ac and H3K27me3 in embryonic stem cells from a public dataset? Which data set may be used to histone modification if we have expression data without doing ChIP-seq. ...
rna-seq written 20 days ago by kanwarjag1.0k • updated 20 days ago by science_lizard0
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Comment: C: Cell type pathway ScRNAseq
... Any comments/ feedback please? ...
written 6 weeks ago by kanwarjag1.0k
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Cell type pathway ScRNAseq
... I am trying to find a toll/ software/ package that can identify cell specific pathways in ScRNA-seq data. I have analyzed the data and has expression matrix per cell type. I googled only two studies – https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6582408/ another issuing RF https://ieeexplore.ieee.o ...
rnaseq pathways written 6 weeks ago by kanwarjag1.0k • updated 6 weeks ago by jared.andrews076.4k
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alternative Pathway analysis
... I have a list of genes from a specific type of cells, Can I perform pathway analysis with any gene expression values? Any suggestion ...
pathway list of genes written 11 weeks ago by kanwarjag1.0k
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Comment: C: Denovo RNA seq
... So If I understand correctly String tie can work with reference as well as without reference -de novo. Just one clarification Do we use Trinity for assembling de novo and then use String tie? ...
written 12 weeks ago by kanwarjag1.0k
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Denovo RNA seq
... I am trying to find which tool or work flow is best/ commonly used for de novo assembly of RNAseq PE data? I want to do two things,. 1. map it back to reference genome and calculate transcript level expression between treatment vs control 2. The unannotated transcripts will be separately accessed an ...
rna-seq written 12 weeks ago by kanwarjag1.0k
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GSEA analaysis understaning
... Can somehow GSEA tell me which gene set is most significantly enriched in our set of analysis. It gives ES, FDRp values. Alternatively, Is there any tool that will give me a ranking of different pathways enriched in my list of genes. ...
pathway written 4 months ago by kanwarjag1.0k
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Single Cell RNAseq of nuclei
... I am generating single nuclei RNAseq and was wondering is there a work flow. How different it may be from single cell RNAseq. There are few work flows reported in google search but it is hard to find out what be best or standard work flow. I thought some one here may like to share their own working ...
rna-seq written 5 months ago by kanwarjag1.0k
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cell ranger tool
... I saw Seurat under R- Shinny as GUI version and was wondering if there is Cell ranger pipeline under GUI that can be used by a person with little programing background. ...
rna-seq written 5 months ago by kanwarjag1.0k • updated 5 months ago by hirad.alipanah10
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Comment: C: Z score and FC
... My apology- P values are there raw p values looks good <0.01 That is the reason I could not grasp what is happening and what to use. Again thanks ...
written 6 months ago by kanwarjag1.0k

Latest awards to kanwarjag

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