User: Bioinfonext

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Bioinfonext150
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Posts by Bioinfonext

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Comment: C: How to extract OTU count information for the selected list of OTU in R
... thanks, sorry for that: I do have OTU Id in first column and sample count like this, I need to extract information for based on selected OTU ids. > head( mymensingh2) leaf-1.S68 leaf-19.S79 673b8e48866a5fdd473f09ad34e0b2c0 5 ...
written 21 hours ago by Bioinfonext150
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How to extract OTU count information for the selected list of OTU in R
... Hi, Could you please suggest to me in `R`, how I can extract count information across all samples for the selected list of `OTU ID` from the OTU table where the first column is OTU ID. I have identified some differential OTU abundance and now for heatmap, I need the count information for these OT ...
R written 22 hours ago by Bioinfonext150
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Difference between PERMANOVA and DESeq2 analysis for amplicon sequencing
... Hi, I am not able to understand what is the difference between `PERMANOVA` and `DESeq2` analysis for `amplicon microbial analysis`. I do have amplicon sequencing data from three treatment condition (T1, T2, and T3) and want to find the taxa which are differential abundant, currently I am using DES ...
R bioconducter written 9 days ago by Bioinfonext150
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Comment: C: How to plot dendrogram based on sample names
... Thanks for your all help and time. ...
written 11 days ago by Bioinfonext150
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Comment: C: How to plot dendrogram based on sample names
... I used genefilter to use only most variable: https://support.bioconductor.org/p/61678/ ...
written 12 days ago by Bioinfonext150
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Comment: C: How to plot dendrogram based on sample names
... thank a lot, could you please also suggest me what this value means here: **518.3202** (q75 <-quantile(rowVars(countMatrix), .75)) 75% 518.3202 ...
written 12 days ago by Bioinfonext150
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Comment: C: How to plot dendrogram based on sample names
... sorry, by mistake I post it again. Thanks bioinfonext ...
written 12 days ago by Bioinfonext150
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How to plot dendrogram based on sample names
... Hi, I do have FPKM count and interested in dendrogram for samples cluster. I used below code but it generate dendogram based on geneID instead of sampleID. > countMatrix = read.table("Trinity_trans.counts.matrix.txt",header=T,sep='\t',check.names=F,row.names=1) > dim(countMat ...
R bioconducter written 12 days ago by Bioinfonext150
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Comment: C: NMDS plot for Amplicon 16s OTU count
... For NMDS, rank-threshold transformation is recommended, but I do not know how to it. I will thankful for your help and time to help me with this. How to do rank threshold transformation for OTU count at a? Thanks ...
written 21 days ago by Bioinfonext150
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NMDS plot for Amplicon 16s OTU count
... I used below code to generate NMDS plot, but I used here raw OTU count as input. prev.ordNMDS_data1 <- ordinate(data1_prev_norm, "NMDS", "bray") plot_ordination(data1_prev_norm, ordination = prev.ordNMDS_data1, color="Region") + theme_minimal() + geom_point(size=5) For NMDS, rank-thre ...
vegan R bioconductor written 22 days ago by Bioinfonext150

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