User: rob.costa1234

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rob.costa1234150
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Posts by rob.costa1234

<prev • 125 results • page 1 of 13 • next >
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trajectories of scRNA-seq
... I have done my part of browsing pubmed and google. I am looking for a very basic paper / blog that may be helpful to understand the concept and interpretation of ScRNAseq trajectories to non computational researchers. Any suggestion? ...
paper written 3 days ago by rob.costa1234150
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Heat map of DE genes identified in Graph based clustering of ScRNA-Seq
... I have scRNA-seq expression matrix (read counts) after graph based clustering. I want to show the clusteras as a heatmap shown in figure 1E or 1F reported in this paper https://www.cell.com/cell-reports/abstract/S2211-1247(18)30339-5 or figure can be accessed directly @ https://ibb.co/mwf16U I w ...
rna-seq heatmap written 9 weeks ago by rob.costa1234150 • updated 8 weeks ago by Michael Dondrup44k
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maintaining a cell lineage population
... I have an RNAseq data of three time points. Day 1 , 3 and 6. Day 1 cells has a specific marker (MYC) and are enriched in specific pathway. The marker (MYC) and pathways got altered when cell reach Day 6 and accordingly change the cell state. My question is if I have to force / maintain these cells ...
rna-seq written 10 weeks ago by rob.costa1234150 • updated 9 weeks ago by Biostar ♦♦ 20
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Mutations in IBD dataset
... Is there a database to study mutations in IBD or crohn's disease? I want to study the level of mutations in one gene. I googled but could not find the one. ...
sequencing written 12 weeks ago by rob.costa1234150 • updated 12 weeks ago by Denise - Open Targets4.7k
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Answer: A: filtering a z score file
... I am also looking how to filter z score file as stated above. Any one here in the forum, has experience working on such files. ...
written 3 months ago by rob.costa1234150
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h5 file of cell ranger
... The h5 file generated - (filtered_gene_bc_matrices_h5 ) by cell ranger pipeline is a normalized data or it is still a raw data? Any suggestion ...
rna-seq written 3 months ago by rob.costa1234150
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cell types for all sequenced data
... If I have a sCRNA seq data, Is it possible to assign each bar code (that is cell) a probable cell type based on expression profile? Are there any tools available for that purpose. If for example 1200 cells sequenced I want to assign each cell a cell type based on human genome. ...
rna-seq written 3 months ago by rob.costa1234150 • updated 3 months ago by Kevin Blighe30k
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Comment: A: plotting a expression data in figure
... Thanks for all suggestions. The purpose of the figure is that I want to show that these 20 genes are deferentially expressed in diseased cases when treated with drug while the same genes are affected to lesser extent or are not affected by drug treatment in healthy animals. ...
written 3 months ago by rob.costa1234150
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plotting a expression data in figure
... I have expression matrix of 20 genes in 5 replicates in healthy vs disease animals treated with a drug. I want to show that the expression level between healthy vs diseased animals ids different. Is there a suggestion how I can put in a figure this information? I can either show correlation but that ...
rna-seq written 3 months ago by rob.costa1234150 • updated 3 months ago by Eric Lim1.1k
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Comment: C: Cell lineage identification from pathway anlaysis
... CIBERSORT need signature genes and provide only LM22 genes as signature for immune cells. It looks lot more complex to draw our own signature from http://fantom.gsc.riken.jp/data/. Thus in the meantime I am just trying to see how the previous cellular deconvolution of micro-array data has evolved. ...
written 3 months ago by rob.costa1234150

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