User: kanwarjag

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kanwarjag1.0k
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United States
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Joined:
7 years, 3 months ago
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Posts by kanwarjag

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6 follow
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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 8 days 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 4 weeks 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 8 weeks ago by kanwarjag1.0k • updated 8 weeks 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 9 weeks ago by kanwarjag1.0k
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Comment: C: Z score and FC
... You are right I have large negative z score with positive FC. How do I calculate |Z| , I googled it but could not find. So what should be considered FC ...
written 9 weeks ago by kanwarjag1.0k
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Z score and FC
... I have results of expression as Fold change and Z score. The Z score is a negative value while FC is >1.2. I was wondering what should be used FC or Z score. I understand that z score is the deviation from mean value and can be plus or minus. ...
rna-seq written 9 weeks ago by kanwarjag1.0k
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Answer: A: what to do after pseudotime analysis by Monocle?
... Though it is an old discussion but I want to add to this discussion my problem- I have performed analysis on single cell RNA-seq data of two samples one is disease vs matched control. IN the diseased sample I want to study the lineage analysis to find out how cells have developed into diseased cells ...
written 9 weeks ago by kanwarjag1.0k
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overlay of DE data on reactome pathway
... I want to overlay my DE of genes data on the Reactome pathway @ https://reactome.org/PathwayBrowser/#/R-MMU-5205647&DTAB=MT The file can be downloaded as SVG/SBGN/ PDF IS there any way that I can first overlay my expression values on the pathway figure and then download the image. Any alternati ...
pathway written 10 weeks ago by kanwarjag1.0k
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question about moncole 2/3
... IS it possible to assign a starting cell type for peusdotime trajectory in Monocle 2 or 3? I am analyzing RNAseq. Could not find on the Monocole manual or on google. ...
rna-seq written 11 weeks ago by kanwarjag1.0k
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GUI based Trajectory tool for RNA-seq
... I am trying to find if there any online GUI based free software that can perform trajectory analysis on single-cell RNAseq. ...
rna-seq written 12 weeks ago by kanwarjag1.0k

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Popular Question 7 weeks ago, created a question with more than 1,000 views. For ncRNA gencode files
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