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Mismatch between gene IDs in Map-SeqNum-ID.txt and HierarchicalGroups.orthoxml

oma orthology pyham written 14 months ago by eschang1 • 10 • updated 14 months ago by adrian.altenhoff • 650

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OMA gene vs splicing variants in the output

orthologs oma orthologs oma pyham written 14 months ago by mateusz.konczal • 0 • updated 14 months ago by adrian.altenhoff • 650

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Pyham - pyham.taxonomy.Taxonomy object by constructing a ete3.Etree

hogs orthoxml pyham written 2.2 years ago by dtejadamartinez • 20 • updated 19 months ago by Christophe Dessimoz • 660

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Recent Replies

A: Importing Newick trees in Cytoscape by conversion to igraph via RCy3 by xanderpico • 210
It looks like you've changed the line. The original is: tree <- phytools::read.newick(sys...
C: The question about the Cytohubba by xanderpico • 210
I don't know if the app authors track questions here or not, but you can find their email contact...
A: Import ontologies into Cytoscape 3.8 Desktop version? by xanderpico • 210
The older versions supported the loading of specific ontologies for data table annotation only ...
C: Import metaphlan output to phyloseq by antonioggsousa • 510
Did you try to convert your biom to text file with biom-convert and them merge then with the merg...
C: BCL2FASTQ2 Pipeline Errors by genomax ♦ 86k
How much memory are you allocating for your job? I suggest you in crease that and try again. You ...
A: Using DESeq2 for time-series analysis by swbarnes2 ♦ 8.0k
Drop that "sample" column. It's pointless. If you want to look for genes that change linearly o...
C: Specifying unequal replicates in deseq2 with htseq-count input by swbarnes2 ♦ 8.0k
Yes. Swapping the input order won't change them alphabetically. You have to relevel or specify ...
C: Import metaphlan output to phyloseq by DC7 • 20
Yes... from metaphlan I get one biom file (with abundance), one abundance file... But biom from q...
C: Illumina polishing after PacBio assembly and polishing? by Chris Fields • 2.1k
> (1) I didn't know that PacBio has systematic deletion at homopolymer regions. Actually as I...
C: Correlate ChIP-seq to gene expression by science_lizard • 0
Thanks for your reply! So if I'm understanding what you mean, I think I've done that kind of anal...
A: Specifying unequal replicates in deseq2 with htseq-count input by kousi31 • 10
Specifying `res <- results(dds, contrast=c("condition","B","A"))` worked. Thank you.
C: Call alternative base for each position in a bam file by sacha • 1.9k
I tried pysamstats by the past . I was thinking it is only for read depths .

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