User: KVC_bioinfo

gravatar for KVC_bioinfo
KVC_bioinfo410
Reputation:
410
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Trusted
Location:
Boston
Last seen:
7 months, 1 week ago
Joined:
2 years, 2 months ago
Email:
k**************@gmail.com

Posts by KVC_bioinfo

<prev • 273 results • page 1 of 28 • next >
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(Closed) R: Stacked bar plot
... Hello all, specie=c(rep("sorgho" , 3) , rep("poacee" , 3) , rep("banana" , 3) , rep("triticum" , 3) ) condition=rep(c("normal" , "stress" , "Nitrogen") , 4) value=abs(rnorm(12 , 0 , 15)) data=data.frame(specie,condition,value) ggplot(data, aes(fill=condition, y=value, x=specie)) ...
R stackedplot written 9 months ago by KVC_bioinfo410
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Comment: C: Bioconductor: quantile normalization
... Thanks! I have looked them. However, I could not find how it works with low expressed genes. ...
written 20 months ago by KVC_bioinfo410
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Bioconductor: quantile normalization
... Hello All, I have used Bioconductor ‘preprocessCore’ fro quantile normalization. I am trying t understand how does it work with low expressed or zero count genes. Is someone aware of that? TIA ...
normalization biocinductor written 20 months ago by KVC_bioinfo410 • updated 20 months ago by Paolo230
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Comment: C: Error while using EdgeR
... I do not have NA. I used quantile normalization using Bioconductor. ...
written 20 months ago by KVC_bioinfo410
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Comment: C: Error while using EdgeR
... edgeR.DGElist <- DGEList(counts = raw.data.m , group = sample_info.edger ) causes error. raw.data.m was a typo sorry about that ...
written 20 months ago by KVC_bioinfo410
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Error while using EdgeR
... Hello All, I am trying to do differential expression using voom package. I constantly get the following error: > Error in .isAllZero(counts) : count matrix must be integer or > double-precision Below is the code I am trying: library(limma) library(preprocessCore) li ...
edger written 20 months ago by KVC_bioinfo410 • updated 7 months ago by Gordon Smyth1.1k
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Extracting longest read from fastq file
... Hello All, I want to extract the longest read from a fastq file. I am not aware of any way to do it. Could someone help me here? TIA ...
fastq written 20 months ago by KVC_bioinfo410 • updated 20 months ago by Pierre Lindenbaum124k
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Changing the legend names: R
... Hello all, ggplot(dataset, aes( x = Norm, fill = Condition, y=log2(measure))) + geom_boxplot() + scale_fill_manual(values=c("brown1","darkolivegreen4","burlywood3")) + theme_classic() + labs(title="Comparison",x="Norm", y = "counts") + scale_fill_continuous(labels ...
R ggplot2 written 20 months ago by KVC_bioinfo410 • updated 19 months ago by Kevin Blighe51k
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Comment: C: error using porechop on nanopore reads
... okay. thank you ill submit an issue there. ...
written 20 months ago by KVC_bioinfo410
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error using porechop on nanopore reads
... Hello all, I am trying to use porechop for adaptor trimming on nanopore reads. I constantly get the following error: Error: input_reads.fastq could not be parsed - is it formatted correctly? I double checked the file. It is fine. I am using the following command: porechop -i input_reads. ...
porechop nanopore written 20 months ago by KVC_bioinfo410

Latest awards to KVC_bioinfo

Popular Question 9 months ago, created a question with more than 1,000 views. For Quartile Normalization in R : RNA-seq
Popular Question 9 months ago, created a question with more than 1,000 views. For installing perl packages.
Popular Question 9 months ago, created a question with more than 1,000 views. For Saving plots in R
Popular Question 9 months ago, created a question with more than 1,000 views. For Adapters fro nano pore sequence
Popular Question 9 months ago, created a question with more than 1,000 views. For Which package to be used for RNA-seq normalization(Limma-voom)
Popular Question 9 months ago, created a question with more than 1,000 views. For Changing the legend names: R
Popular Question 9 months ago, created a question with more than 1,000 views. For Error while installing RSeQC
Popular Question 9 months ago, created a question with more than 1,000 views. For Quantile Normalization in R
Popular Question 9 months ago, created a question with more than 1,000 views. For Bowtie2: gtf file - annotation file
Student 9 months ago, asked a question with at least 3 up-votes. For Post alignment QC of RNA-seq data
Great Question 13 months ago, created a question with more than 5,000 views. For Changing the legend names: R
Popular Question 13 months ago, created a question with more than 1,000 views. For Quartile Normalization in R : RNA-seq
Popular Question 13 months ago, created a question with more than 1,000 views. For Error while installing RSeQC
Popular Question 13 months ago, created a question with more than 1,000 views. For installing perl packages.
Popular Question 13 months ago, created a question with more than 1,000 views. For Which package to be used for RNA-seq normalization(Limma-voom)
Popular Question 13 months ago, created a question with more than 1,000 views. For how to make a .tbi file of .gtf.gz?
Popular Question 13 months ago, created a question with more than 1,000 views. For Genome and Transcriptome as a reference
Popular Question 13 months ago, created a question with more than 1,000 views. For Extracting randomly subset of fastq reads from a huge file
Popular Question 13 months ago, created a question with more than 1,000 views. For Adapters fro nano pore sequence
Popular Question 13 months ago, created a question with more than 1,000 views. For Extract reads from fasta file (specific read_names)and make a new fasta file
Popular Question 13 months ago, created a question with more than 1,000 views. For Downloading annotation file for human transcriptome
Popular Question 13 months ago, created a question with more than 1,000 views. For Human transcriptome download
Popular Question 13 months ago, created a question with more than 1,000 views. For Quantile Normalization in R
Popular Question 13 months ago, created a question with more than 1,000 views. For Viral integration with RNA-seq data
Popular Question 13 months ago, created a question with more than 1,000 views. For Changing the legend names: R

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