Moderator: cpad0112
cpad0112 ♦ 13k
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Posts by cpad0112
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Comment:
C: RNA seq data analysis
... Follow the comprehensive RNAseq tutorial from Griffith lab: https://github.com/griffithlab/rnaseq_tutorial ...
written 1 day ago by
cpad0112 ♦ 13k
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3
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102
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3
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... try gnu-parallel or bash arrays. ...
written 2 days ago by
cpad0112 ♦ 13k
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20k
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1
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... look at the bottom figures of https://digibio.blogspot.com/2020/07/control-grouped-barcharts-in-ggplot.html ...
written 3 days ago by
cpad0112 ♦ 13k
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90
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... did you use biom to sff convert script provided by stamp team? ...
written 3 days ago by
cpad0112 ♦ 13k
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90
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... `f__Clostridiales_unclassified` ...
written 4 days ago by
cpad0112 ♦ 13k
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90
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... f stands for family and g stands for genus in example line. IN example line 6 levels of information is present. I guess 7th level, species is not pasted. Please post the `some error` here to understand what is going on. please also post few lines output from metaphlan and the how you are executing ...
written 4 days ago by
cpad0112 ♦ 13k
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334
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... we did it with 16s with megan. But due to licensing issues, we shifted to qiime2 pipeline. If you are new, you can follow this protocol (galaxy and mothur): https://galaxyproject.github.io/training-material/topics/metagenomics/tutorials/mothur-miseq-sop/tutorial.html ...
written 5 days ago by
cpad0112 ♦ 13k
0
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84
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... From the code, it seems earlier dev used DESeq2 analysis. Please follow the manual of DEseq2 here: http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#heatmap-of-the-count-matrix ...
written 6 days ago by
cpad0112 ♦ 13k
1
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1
answer
94
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... Use zero length assertions in R. Without zero length assertions:
# Protein sequences used in searching
> pepseq=c("AVFQLLDSMGPSLPIAEYIASLDRPR","DAIPAVEVFEGEPGNK")
# Protein sequences to be searched against
> pepseq1=c("OAAAADDAIPAVEVFEGEPGNK","CDDDDDDPDAVFQLLDSMGPSLPIAEYIASLDR ...
written 9 days ago by
cpad0112 ♦ 13k
0
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126
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1
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... apply(mymatrix, 1, function(x) t.test(x[24:35],x[36:39], paired=FALSE)$p.value ...
written 9 days ago by
cpad0112 ♦ 13k
Latest awards to cpad0112
Appreciated
5 days ago,
created a post with more than 5 votes.
For A: Analysis past the differentially expressed genes: RNAseq
Scholar
7 days ago,
created an answer that has been accepted.
For A: .fai file generation for a vcf file containing snps
Appreciated
10 days ago,
created a post with more than 5 votes.
For A: Analysis past the differentially expressed genes: RNAseq
Appreciated
23 days ago,
created a post with more than 5 votes.
For A: Analysis past the differentially expressed genes: RNAseq
Commentator
24 days ago,
created a comment with at least 3 up-votes.
For C: Problem installing Rgraphviz in R
Teacher
25 days ago,
created an answer with at least 3 up-votes.
For A: convert SNP calls to amino acid change
Commentator
5 weeks ago,
created a comment with at least 3 up-votes.
For C: Problem installing Rgraphviz in R
Teacher
5 weeks ago,
created an answer with at least 3 up-votes.
For A: convert SNP calls to amino acid change
Scholar
5 weeks ago,
created an answer that has been accepted.
For A: .fai file generation for a vcf file containing snps
Teacher
7 weeks ago,
created an answer with at least 3 up-votes.
For A: convert SNP calls to amino acid change
Scholar
7 weeks ago,
created an answer that has been accepted.
For A: .fai file generation for a vcf file containing snps
Teacher
7 weeks ago,
created an answer with at least 3 up-votes.
For A: convert SNP calls to amino acid change
Appreciated
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created a post with more than 5 votes.
For C: can someone read this result to me
Scholar
8 weeks ago,
created an answer that has been accepted.
For A: .fai file generation for a vcf file containing snps
Appreciated
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created a post with more than 5 votes.
For C: can someone read this result to me
Scholar
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For A: .fai file generation for a vcf file containing snps
Commentator
11 weeks ago,
created a comment with at least 3 up-votes.
For C: Problem installing Rgraphviz in R
Popular Question
12 weeks ago,
created a question with more than 1,000 views.
For GATK variant calling for RNAseq data between groups
Teacher
12 weeks ago,
created an answer with at least 3 up-votes.
For A: convert SNP calls to amino acid change
Scholar
3 months ago,
created an answer that has been accepted.
For A: .fai file generation for a vcf file containing snps
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4 months ago,
created a comment with at least 3 up-votes.
For C: Problem installing Rgraphviz in R
Commentator
4 months ago,
created a comment with at least 3 up-votes.
For C: Problem installing Rgraphviz in R
Appreciated
5 months ago,
created a post with more than 5 votes.
For C: can someone read this result to me
Teacher
5 months ago,
created an answer with at least 3 up-votes.
For A: convert SNP calls to amino acid change
Scholar
5 months ago,
created an answer that has been accepted.
For A: .fai file generation for a vcf file containing snps
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