User: Bioinformatics

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Posts by Bioinformatics

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Comment: C: make a dash instead those gene that do not have ortologue
... @Mike Smith thanks this is difently helpful but in case if the gene names exist and similar in both. do you know what I am trying to do? I am trying to find the orthologue of a mouse gene. is there a possibility to evaluate them based on chromosome or DNA level? how people evaluate the orthologue to ...
written 21 hours ago by Bioinformatics20
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make a dash instead those gene that do not have ortologue
... I want to convert a set of genes which I can use the biomart to convert them      musGenes <- c("Hmmr", "Tlx3","STSRAAA1", "Cpeb4")     convertMouseGeneList <- function(x){     require("biomaRt")     human = useMart("ensembl", dataset = "hsapiens_gene_ensembl")     mouse = useMart("ensembl", ...
biomart written 1 day ago by Bioinformatics20 • updated 1 day ago by Mike Smith2.5k
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how to create index
... how can i use Rsubread​ to make the index based on human reference? i could not find the command  In their documentation, I can see the following  ref <- system.file("extdata","reference.fa",package="Rsubread") buildindex(basename="reference_index",reference=ref)​ but I don't know how to build ...
rsubread written 9 days ago by Bioinformatics20 • updated 9 days ago by Mike Smith2.5k
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Comment: C: what happened in limma or Desq2 for ANOVA
... actually one ignores the intercept and one involve the intercept . I am wondering which way is the right way to do ?  ...
written 27 days ago by Bioinformatics20 • updated 27 days ago by Gordon Smyth32k
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what happened in limma or Desq2 for ANOVA
... I know that for limma we use the following for when we have 2 control and 2 treated design <- model.matrix(~c(rep(0,2),rep(1,2))) and for Deseq2 condition <- factor(c("Control","Control","Treated","Treated"))   Now I have this questions one specifically for limma  1- does it matter i ...
limma written 28 days ago by Bioinformatics20 • updated 27 days ago by Gordon Smyth32k
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Comment: C: how to analysis htseq-count
... @Michael Love Do you tihnk that htseq-count is ok for expression analysis? what if I take log2 of htseq-count and then use limma? the problem with your package is that i cannot follow the parts due to the fact that you have created a table inside your package. I am pretty good at R , I just want to ...
written 28 days ago by Bioinformatics20
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Comment: C: how to analysis htseq-count
... @Michael Love Thanks, I have read but still could not use it properly. should I follow from 4.2 Starting from count matrices ? my question is that I have put together the samples and so I have one column with my gene ID and 40 columns of counts (20 conrtol and 20 treated) Can you please tell me from ...
written 28 days ago by Bioinformatics20
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how to analysis htseq-count
... I am trying to analysis 40 samples htseq-count data (20 healthy and 20 diseases) with deseq2 I have read the manual of the package but I have the data ready in my workspace . It is a dataframe of 30000*40  The first 20 columns are my healthy and the second 20 are the diseases  Is there anyone who ...
deseq2 written 28 days ago by Bioinformatics20 • updated 28 days ago by Michael Love16k
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Comment: C: how can I configure my proxy to get connected to biomart
... @Mike Smith can you tell me how for example use those information to get through ? I have safari  ...
written 4 weeks ago by Bioinformatics20
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Comment: C: how can I configure my proxy to get connected to biomart
... @Mike Smith it gives me this  <MartRegistry> <MartURLLocation database="ensembl_mart_91" default="1" displayName="Ensembl Genes 91" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_ENSEMBL" path="/biomart/martservice" port="80" serverVirtualSchema="default" visib ...
written 4 weeks ago by Bioinformatics20

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