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Use of OrthoFinder pipeline

species tree ortholog prediction phylogenomics written 3 months ago by basusudipto92 • 0

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2.7k

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map gene gain loss on species tree

reconciliation species tree gene tree written 4.8 years ago by Anand Rao • 310 • updated 3 months ago by xmuraji • 0

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365

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Building gene trees

bucky species tree astral gene tree written 10 months ago by Colaptes • 40 • updated 9 months ago by Brice Sarver • 3.5k

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226

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STRAW & MP-EST tree

species tree gene tree written 10 months ago by najmehparvaz • 0

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501

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Clarification of OMA tree metrics

orthologs oma species tree written 19 months ago by samche42 • 0 • updated 11 months ago by Biostar ♦♦ 20

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560

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R: apex Multigene alignment problems "DNA sequences in list not of the same length"

apex R astral species tree multigene alignment written 19 months ago by samche42 • 0

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Recent Replies

C: Featurecounts to DESEq2 - How to merge biological replicates? by Kyle • 80
Hi: For my understanding. Read.delim can only read 1 txt file once. I have used this when using e...
C: Getting coding sequence length by lieven.sterck ♦ 8.0k
without the actual CDS coordinates ( structural annotations ) , it will be quite hard . Don't yo...
C: type='apeglm' shrinkage only for use with 'coef' by igor ♦ 11k
The [DESeq2 vignette][1] has a table summarizing the different types ("Extended section on shrink...
C: Cluster sub-set analysis using Seurat by igor ♦ 11k
> the raw count table are the same either way Clustering is not based on the raw counts table...
C: Cluster sub-set analysis using Seurat by igor ♦ 11k
What is a geometric analysis?
C: Cluster sub-set analysis using Seurat by igor ♦ 11k
Subsetting just keeps/removes specific cells. It does not alter their metadata.
A: Getting the assembled genome using the BAM file obtained from reference mapping by h.mon ♦ 30k
To get an assembled genome, you need to assemble the reads, not map them onto a reference genome....
A: Trimmomatic and Salmon error by Rob ♦ 4.0k
It looks like you have an inconsistent set of modules loaded on the nodes where younare running? ...
A: volcano plot help code by Kevin Blighe ♦ 61k
Did you create this github issue? - https://github.com/kevinblighe/EnhancedVolcano/issues/52 Try...
C: METAPHLAN: Getting genus level resolution but not family level by DC7 • 20
I am not getting any script to merge all the metaphlan `.biom` outputs which I should do prior to...
C: Differential Expression analysis between single cell RNa seq & bulk RNa seq data by bioyas • 0
As you said it does not make sense to do this analysis without modification.. IF we do DE without...
C: Cluster sub-set analysis using Seurat by singcell • 0
Thank you for your reply. I have got integrated Seurat object containing KO and WT samples. Can I...

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