User: Jaan

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Jaan0
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Posts by Jaan

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Comment: C: How to pick the longest splice variants sequence from a fasta file?
... Thanks for the guide. I definitely like to learn programming even though i new in this field, but i am doing my best with slow progress.   ...
written 4.6 years ago by Jaan0
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How to pick the longest splice variants sequence from a fasta file?
... Hi every one, I have a data example like follow, and i have to select the splice variant which has the longest prot. sequnces and remove the rest from my.fasta file. my.fasta file has 32000 protein sequences and also contains 1023 splice variants. >Bpen|evm.model.Contig148.21 <===(splice va ...
gene R next-gen sequencing genome written 4.6 years ago by Jaan0 • updated 4.6 years ago by Devon Ryan90k
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Comment: C: How to Write a loop for a big matrix?
... Thanks for the heads up, yes i was having the same doubt, and i was searching for a way to over come that EM Algorithm, which looks to whole data set. By the way, i am running this data set on our server (100 GB memory). I did not use rm(eset, df) because i taught i have enough space if i dont, but ...
written 4.8 years ago by Jaan0
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Comment: C: How to Write a loop for a big matrix?
... Thanks for the interest. No i dont need to put the eset (an expression set from Microarray data) nor df in the memory, as soon as i convert it to a matrix (X) version. ...
written 4.8 years ago by Jaan0
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How to Write a loop for a big matrix?
... Hi every one, I have a matrix with 21492 columns and 8532 rows. i am running flexmix package to calculate Gaussian univariate distributions. When i run the following commands the process will crash due to lack of memory, but if i run the first 5000 column [X <- as.matrix(df[,1:5000])] only,  i g ...
R written 4.8 years ago by Jaan0
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How to retrieve all the possible RNA-seq data sets from public data bases?
... Hi I have a task which i have to collect every possible sets of RNA-seq data from a public database (GEO, ArrayExpress, etc) for Arabidopsis thaliana, and start to look for some analysis on them. Mean while, i tried GEOquery and ArrayExpress packages in R, but what i get is a .soft file, which is ...
R next-gen rna-seq sequencing written 4.9 years ago by Jaan0 • updated 4.9 years ago by Matt Shirley9.0k

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