Moderator: cpad0112

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cpad011213k
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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 cpad011213k
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Comment: C: How do I use bash loop to map with Salmon on files in multiple folders
... try gnu-parallel or bash arrays. ...
written 2 days ago by cpad011213k
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Comment: C: geom_bar plot with several variables
... look at the bottom figures of https://digibio.blogspot.com/2020/07/control-grouped-barcharts-in-ggplot.html ...
written 3 days ago by cpad011213k
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Comment: C: METAPHLAN: Getting genus level resolution but not family level
... did you use biom to sff convert script provided by stamp team? ...
written 3 days ago by cpad011213k
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Comment: C: METAPHLAN: Getting genus level resolution but not family level
... `f__Clostridiales_unclassified` ...
written 4 days ago by cpad011213k
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Comment: C: METAPHLAN: Getting genus level resolution but not family level
... 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 cpad011213k
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Comment: C: Rarefaction curve of Shotgun metagenome
... 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 cpad011213k
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Comment: C: RStudio Pheatmap: sort DEG by logFC
... 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 cpad011213k
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Comment: C: Fasta Files - How to search for peptide sequences?
... 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 cpad011213k
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Comment: C: p value from multiple columns using R??
... apply(mymatrix, 1, function(x) t.test(x[24:35],x[36:39], paired=FALSE)$p.value ...
written 9 days ago by cpad011213k

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 8 weeks ago, 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 8 weeks ago, created a post with more than 5 votes. For C: can someone read this result to me
Scholar 9 weeks ago, created an answer that has been accepted. 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
Commentator 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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