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### Issue: `ValueError: No objects to concatenate` during `motif_enrichment_dem` Execution
```bash
scenicplus grn_inference motif_enrichment_dem \
--region_set_folder /n/sci/SCI-004375-NYUDATA/…
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Dear Dr. Derelle,
Thank you for your work with Broccoli.
Quick question, is there support for a user-supplied blast directory, like `orthofinder -b`? I'd like to port my orthology pipelines to Bro…
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Self-assigning this one, if that's OK with everyone. Results should be an updated mapping.py file and a new loader for DIOPT.
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In semi-model organisms, NCBI and Ensembl usually provide annotations based on ab initio gene prediction and orthology based evidence. With cheap RNAseq, we can build RNA based gene models using Cuffl…
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In addition to PRO-short-label, make PRO-org-label that will use the specific organism's gene name instead of the orthology based one.
First, verify that the labels will be correct. Might need to r…
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Hi Carlos,
First off, thank you so much for putting in all of the work to develop this tool. I have been looking for something similar to this for years and I finally need to publish some papers …
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Hello!
I would like to make a heatmap of the abundances of KOs that are linked to the significantly enriched pathways across all of my samples. Is there a way to do this using FMAP? For example, if…
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This step is to provide a ground state assessment of what pathways for orthology projections look like that are imported from Reactome. Decisions to be made:
- [x] which species?
- [x] All pathways o…
ukemi updated
10 months ago
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In GitLab by @fbastian on Apr 19, 2016, 16:06
Rough figure of workflow for multi-species analyses in bgee-core:
[multispe_workflow.pdf](https://gitlab.isb-sib.ch/Bgee/bgee_apps/uploads/cee5900a69…
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different types of users would like different reporting structures across the data.
For a program officer, perhaps a graph showing accumulation of model organisms of X,Y,Z species that have asserted…