User: rob.costa1234

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rob.costa1234180
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Posts by rob.costa1234

<prev • 132 results • page 1 of 14 • next >
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Marker genes for a cell type in ScRNA
... In single-cell RNA-seq. if I have to assign marker genes to a specific cell type. To do so- That marker gene will be present only in one cluster of one cell type and not any other cell type? Do we see the relative expression of marker genes and if that gene is upregulated in one cluster, that may b ...
rna-seq written 10 hours ago by rob.costa1234180 • updated 9 hours ago by igor8.3k
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KM plot from different public datasets
... I have 4 different data sets of same disease with No of days of survival and death. I want to correlate this data with gene expression of my study. Can I used 4 different data sets based on high and low expression of my genes and survival and death in each datsets and club them together for presenta ...
km plot written 2 days ago by rob.costa1234180
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Interpret Cbioportal output
... I performed simple mRNA expression of a particular gene and then looked for survival curve in However survival curve has two grps case without alterations in query gene and second cases with alterations in query gene. I looked around the tutorial FAQ of Cbio-portal, Google it but could not find the ...
sequence rna-seq written 7 days ago by rob.costa1234180 • updated 7 days ago by WouterDeCoster41k
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iPSC gene expression database
... Is there any database for iPSC gene expression from RNA-seq or Array for different organisms- human, mouse etc.? I am looking something for iPSC similar to TCGA data-sets. ...
database rna-seq written 10 weeks ago by rob.costa1234180
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Identification of different bacterial strains in mixed population Sequencing
... I want to identify different bacteria in a microbial mixed population using non-16Srna regions. I have two questions- 1. Is there any alternative approach out there may be based on consensus sequence or marker genes of different bacteria or anything else. Most of publications are based on 16sRNA b ...
sequencing written 6 months ago by rob.costa1234180
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DBSCAN clustering in GUI or online software
... Is there any web based or GUI based tool that has Density-based spatial clustering (DBSCAN) r package option for clustering. It has to be recommended to a non bioinformatic colleague to explore. Thanks ...
gui version web based written 7 months ago by rob.costa1234180 • updated 7 months ago by Jean-Karim Heriche20k
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Question about selection of pathways to inhibit
... I have an RNAseq results of drug treated vs control cells and performed pathways analysis with Up an down regulated genes. What I am trying to find is which pathway is up-regulated so that it is inhibited with selected inhibitors. The question – is it possible to find which pathways are up-regulated ...
pathways written 10 months ago by rob.costa1234180
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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 11 months ago by rob.costa1234180
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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 13 months ago by rob.costa1234180 • updated 13 months ago by Michael Dondrup46k
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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 13 months ago by rob.costa1234180 • updated 13 months ago by Biostar ♦♦ 20

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