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167

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Working in R with HTS cluster analysis data

vegan R hts metabarcoding tidyverse written 3 months ago by edoardoscali.93 • 0

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839

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Relative abundance in phyloseq and biplot

vegan phyloseq r bioconducter written 8 months ago by Bioinfonext • 320

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279

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PCoA plot with phyla abundance

vegan R phyloseq written 10 months ago by Bioinfonext • 320

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394

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Vegan beta diversity and permutation analysis

vegan R bioconducter written 18 months ago by Bioinfonext • 320 • updated 10 months ago by Biostar ♦♦ 20

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572

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NMDS plot for Amplicon 16s OTU count

vegan R bioconductor written 19 months ago by Bioinfonext • 320

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948

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Microbiome data analysis using Vegan R tool

vegan microbiome written 2.4 years ago by MAPK • 1.7k • updated 2.3 years ago by Biostar ♦♦ 20

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551

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Variation partitioning using latitude and longitude as explanatory variables

vegan R written 3.0 years ago by ieie • 10

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2.5k

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Stuck on calculating principal components

vegan R snp software error written 3.1 years ago by A • 3.9k • updated 3.1 years ago by pfs • 280

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1.7k

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Removal of rare OTUs before calculating community distances / ADONIS / NMDS

vegan microbiome 16s adonis nmds written 4.4 years ago by dmcleanuk • 10

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1.2k

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Replicates in Canonical Correspondence Analysis or PERMANOVA

vegan metabarcoding R written 4.5 years ago by lelle • 830

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8.0k

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How to plot UniFrac PCoA with 95% confidence Elipses in R

vegan R metagenomics phyloseq ordiellipse written 6.0 years ago by c.v.oflynn • 100 • updated 5.8 years ago by Biostar ♦♦ 20

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Recent Replies

C: What does p-value mean ? What and how can i interpret the results by _r_am ♦ 32k
I agree with both your points but saying "Google search should give you a bunch of articles" is b...
C: How to avoid building millions of BWA indices? by Pierre Lindenbaum ♦ 132k
> . Is there a way to somehow merge BAM files so I can save time from building BWA indices eac...
C: recent Hi-C databases by Bogdan • 1.1k
thanks a lot, very very helpful !
A: recent Hi-C databases by jared.andrews07 ♦ 8.3k
[This list](https://github.com/mdozmorov/HiC_data) on github is a pretty good one in terms of dat...
A: Trimmomatic couldn't generate output file by swbarnes2 ♦ 9.3k
For starters, I would not give your outputs the same name as your inputs! You need to keep input...
C: Meta-analysis of two datasets. by parveenkayenat • 0
The data is the result of GWAS of quatitative traits. I want to perform meta-analysis on those tw...
A: Getting all the genomic coordinates where RNA-seq reads are split within a given by Pierre Lindenbaum ♦ 132k
> I thought of trying something simple as obtaining all the coordinates in which the RNA-seq r...
C: Best-suited unit of expression to perform between-sample comparison by spaladug • 10
You should use TPM values for within sample comparison.
C: bedtools shuffle with adjustment of GC ratio by zekexu • 0
Hi Dr. Guo, Wondering if you have found a feasible solution? Or how to define the GC% range? I m...
C: STAR --quantMode GeneCounts vs HTSeq-count by Uday Rangaswamy • 150
Thanks. The count file of both the tools matched when I sorted it wrt name instead of the default...
C: ATAC-seq annotation to gene names by i.sudbery ♦ 10k
The inTad package, linked in my answer, is an R package. I'm sure you can do the other two meth...
A: ATAC-seq annotation to gene names by RHI • 0
Thank you so much. Is there a way I can do the same using R? Is there any package/function would ...

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