User: qicaibiology

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qicaibiology40
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Posts by qicaibiology

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binomial test questions on determine the intron retention from reads on #E1I, #I and #IE2
... Hi everyone: I am recently reading a [paper][1] on intron retention analysis, there are several places I have not figured out myself what does it mean, one example is like this: In order to determine if an intron retention is real from the reads number among E1I(exon1intron junction), I(intron), a ...
R rna-seq written 4 weeks ago by qicaibiology40
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Answer: C: Failed to install package(ASpli) in R
... My friend and I checked the errors. What we did is : `install.packages('Matrix')` Then we install ASpli again, and it does not show error. Going to give it a run to see what is going on. Thanks for your help ...
written 5 weeks ago by qicaibiology40
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Comment: C: Failed to install package(ASpli) in R
... it does not work out in the end. I can not even library(ASpli) in the end. Looks that it still has the same problem. "`> library(ASpli)` > Loading required package: parallel Loading required package: edgeR > Loading required package: limma Error: package or namespace load > failed for ...
written 5 weeks ago by qicaibiology40
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Comment: C: Failed to install package(ASpli) in R
... this is what I got : (base) [caiqi@midway2-login2 ~]$ conda activate R-3.6-env Could not find conda environment: R-3.6-env You can list all discoverable environments with `conda info --envs`. (base) [caiqi@midway2-login2 ~]$ conda info --envs # conda environments: # ...
written 5 weeks ago by qicaibiology40
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Comment: C: Failed to install package(ASpli) in R
... I tried your method, and I went into R and get the following: > library(ASpli) Loading required package: parallel Loading required package: edgeR Loading required package: limma Error: package or namespace load failed for 'edgeR' in dyn.load(file, DLLpath = DLLpath, ...): ...
written 5 weeks ago by qicaibiology40
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Comment: C: Failed to install package(ASpli) in R
... Thank your very much for your reply! I am trying your code to see what will happen. Can I ask another question because I don't understand very well about it: I saw I have anaconda2 folder and it contains lib which contains R : anaconda>lib>R, and I saw some packages in the R like edgeR and som ...
written 5 weeks ago by qicaibiology40
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Failed to install package(ASpli) in R
... Hi all: I am working through a terminal on the computation center in the University. Recently, I need to install a package in R to analyze my RNA-seq data. I am under the anaconda2 environment. So I use `conda install R` to install R and call R by typing `R`. However, when I tried to install ASpli ...
software error R rna-seq written 5 weeks ago by qicaibiology40
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Comment: C: Differential gene expression from 1 replicate using RPKM and edgeR
... Thank you for your detailed and patient explanation, I modified the code according to your advice and get it work. At the same time get a deeper understanding of the comparison. The manual I used is here ([Manual][1]) from page 7 to 8 it said when using the filter function from edgeR, it uses the C ...
written 7 weeks ago by qicaibiology40
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Comment: C: Differential gene expression from 1 replicate using RPKM and edgeR
... I ran through the steps in the manual, but get no significant changed genes. I can not figure out which part is wrong. my code are listed as: setwd("/Users/cqi/Desktop/kdm5bkd/") files <- c("shCTRRep1.txt", "shCTRRep2.txt", "shKdm5bRep1.txt", "shKdm5bRep2.txt") read.delim(files[1], n ...
written 7 weeks ago by qicaibiology40
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Comment: C: Differential gene expression from 1 replicate using RPKM and edgeR
... Thanks for your advice. But I saw in the manual that the raw count need to be transformed into CPM? Do you think it is not necessary? Thanks, ...
written 7 weeks ago by qicaibiology40

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