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I have generated KEGG KO annotation results (_woltka classify_) and pathway results (_woltka collapse_ on KO results), and finally pathway coverage results (_woltka coverage_ on KO results with KEGG `…
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First off, incredible thanks for the developing this software suite! I've been struggling with calculating KEGG module completion ratios (MCR) at scale ever since KEGG removed their MAPLE software bu…
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I runned this script:
library(readr)
library(ggpicrust2)
library(tibble)
library(tidyverse)
library(ggprism)
library(patchwork)
# Load necessary data: abundance data and metadata
abundance_f…
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See http://www.home.ndexbio.org/data-model/
- Use context to abbreviate identifiers namespaces
```
"context":[{
"ncbigene" : "http://identifiers.org/ncbigene/",
"kegg.pathway" : "ht…
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Question: Is there a, general, expected runtime for the KEGG database connection step of the pathway_annotation() command?
This is my first time using the package, and I am passing (what I think i…
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Hello there,
I noticed that the `download_KEGGfile` function is currently not working.
When I am trying to run `download_KEGGfile(pathway_id="00010", species="eco", target_dir = getwd())`, only th…
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Use `getPathwayIdsPerCompound()`.
Add a limitation to the number of pathways.
See pkrog/biodb#404
Add to the data frame:
* [ ] Pathway IDs.
* [ ] Pathway Names.
* [ ] Pathway Classes (the mo…
pkrog updated
4 years ago
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error:
```php
Step 1: Preloading File sites/all/modules/custom/tripal_analysis_kegg/kegg.obo...
array_key_exists(): The first argument should be either a string or an integer OBOImporter.inc:22…
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We only get parts of CTD, do we want more? Additionally, the parser has a reference to 'RO:0001001' (derives_into) but the code prevents that predicate from ever occurring, the get_chemical_label_id f…
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Hi! I´m trying to do some analysis using the tool pathway in Rstudio, but I have a problem. When I search my micoorganism in kegg it looks like there´s no problem:
> #search_kegg_organism('psav', …