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Dendrogram on SNPs from VCF file?

snphylo fasttree snprelate written 19 months ago by popescuiofelia • 10 • updated 16 months ago by sankar2004 • 10

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SNPhylo does not obey number of autosome chromosomes

snphylo written 3.7 years ago by viniciushs.z • 20 • updated 2.1 years ago by nataliagru1 • 50

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SNPhylo Error Help: there is no SNP and Na/NaN arguement

phylogenetic vcf snphylo tree written 4.1 years ago by N Smith • 10 • updated 4.0 years ago by Biostar ♦♦ 20

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Recent Replies

A: how to define cis regulatory elements using histone modifications ChIPseq by ATpoint ♦ 38k
>why are H3K27ac peaks broad It is not, it is a classical narrow histone mark. > 2: Peopl...
C: RPKM and TPM when operating with small group of genes: is there a bias? by Macspider • 3.1k
In my workflow, the reads are mapped to certain known genes of a metagenome. While I cannot inclu...
C: RPKM and TPM when operating with small group of genes: is there a bias? by Gautier Richard • 300
I don't think that RPKM or TPM are meant to be calculated for a handful of genes, you need to com...
C: How to avoid overfitting using SVA? by Sam • 30
To me personally it seems that once we perform SVA, we introduce an unverified assumption to the ...
C: What is the most appropriate design matrix for paired samples and two disease st by M.ap • 0
It looks like we're in the same group
C: How does salmon deal with decoy? by Assa Yeroslaviz • 1.4k
Thanks, it sounds logical and straightforward. Is this something specific for Salmon, or does Kal...
C: How to convert the ordinal categorical trait in the WGCNA? by tianqi.ma1994 • 0
I have a similar question with you but my clinical traits is cell development timepoint (Day0, Da...
C: Will it be fine if the benchmarking of an assembler/aligner is performed using a by JC ♦ 11k
What do you mean? For assemblers is common to benchmark using different library sizes with severa...
C: TopGO gene enrichment analysis with predefined set of genes for non-model organi by Ambika • 30
Yes I want the p-values and the gene id (FUN__) in my results, which I am not getting. Thank you ...
C: How to read a dataframe into Seurat for AddMetaData properly? by Pratik Mehta • 30
That worked with scfp <- AddMetaData, Gosh, silly mistake... but now problem is the MetaData d...
C: TopGO gene enrichment analysis with predefined set of genes for non-model organi by Kevin Blighe ♦ 65k
As far as I understand, the code is running but you want 'raw' p-values for the GO terms (?) or t...
C: TopGO gene enrichment analysis with predefined set of genes for non-model organi by Ambika • 30
Kevin, I think I do have a list as mentioned in the protocol. The list looks like this > ...

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