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老师好,感谢您分享的脚本,我很幸运在做比较基因组时遇见了您的教程,这给我了很大的帮助。
我在运行[gene_family_summary.R]https://github.com/xieyichun50/coral_genome_Catalaphyllia_jardinei/blob/main/scripts/gene_family_summary.R
我没找到Orthogroup.sta…
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Hello,
I am running Orthofinder on 276 species of insects with the default settings (orthofinder.py -f /directory). This is the message I got after writing orthogroups to file: ```
2023-01-31 …
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Going through the analysis pipeline, after generating Orthogroups and converting the original gxc to exc matrices, it turns out that some Orthogroups end up with the exact same expression values. This…
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> True, most of them are on par with the transcriptomes in the other study- the P. cordata and P. jahnii transcriptomes are the two with the lowest proportion of genes in core orthogroups (but similar…
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Good morning,
I am working on a project to understand how a particular trait influences the number of genes under positive selection, at the level of the genome, and am using BUSTED-PH.
I have…
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**Describe the bug**
I'm trying to run javascript with doJavaScript, but i t throws a com error.
**To Reproduce**
Just run the example: https://loonghao.github.io/photoshop-python-api/examples/#e…
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Would be really nice to have a visual summary of various steps in the pipeline using Sankey diagrams, e.g. via [plotly](https://plotly.com/python/sankey-diagram/). Some diagram ideas:
- Flowchart o…
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Hi David,
I have run OrhoFinder `2.5.4` on the example data with the `-y` option and otherwise default parameters. The HOGs in the file `Phylogenetic_Hierarchical_Orthogroups/N0.tsv` for the orthog…
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Hi David,
I was recently using OrthoFinder to look for species-specific orthogroups in a new genome that we've assembled. However, I noticed that several of the orthogroups classified as species-sp…
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In the REFERENCE_pangenes.txt output file, we have 27000 unique orthogroups ('og' column, syntenic and non-syntenic orthologs).
However after running query_pangenes(gsParam, refGenome = "REFERENCE"…