User: rob.costa1234

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rob.costa1234200
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Posts by rob.costa1234

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Comment: C: Cellular development RNAseq
... For pseudotime we assign one population as starting and map rest where they can map. If I start with a mixed population from where a specific cell type may arise, and I don’t know the start which mapping should be best. I can look for some marker genes, but how can I make sure the correct order of d ...
written 29 days ago by rob.costa1234200
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Cellular development RNAseq
... In single-cell RNAseq, when we use any pseudotime/ trajectory analysis it gives us cellular physiological state. Is it possible to stack a heterogeneous population into an order of there development in that particular treatment? To further expand on the question- I have one sample diseased vs one co ...
rna-seq written 4 weeks ago by rob.costa1234200 • updated 22 days ago by Biostar ♦♦ 20
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Down regulated genes in sC-RANseq
... In single cell RNAseq do we also list down regulated genes as key signature genes of a particular cell type? Thanks. ...
rna-seq written 6 weeks ago by rob.costa1234200
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Chicken embryo annnotations
... Before I do any analysis on a dataset, I got stuck with one question about sample annotations. There is one GEO dataset of RNAseq from an embryo that has annotations like : E6.5_embryo2_sc15; E6.5_embryo2_sc16; E6.5_embryo1_sc40. That means these are replicates of the same embryo or else. I am tryin ...
rna-seq written 4 months ago by rob.costa1234200
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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 5 months ago by rob.costa1234200 • updated 5 months ago by igor9.6k
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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 5 months ago by rob.costa1234200
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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 5 months ago by rob.costa1234200 • updated 4 months ago by gable_works40
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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 7 months ago by rob.costa1234200
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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 11 months ago by rob.costa1234200
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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 12 months ago by rob.costa1234200 • updated 12 months ago by Jean-Karim Heriche21k

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