Could not find function "ti_monocle3"

[akattapuram-insitro]

Hi! I was following the tutorial for running an evaluation of TI methods: https://dynverse.org/developers/evaluating-ti-method/. I wanted to run this with monocle3, but it is giving me a could not find function error.

Code:

library(zellkonverter)

data <- readRDS('cortical-interneuron-differentiation_frazer.rds')

library(dyneval)

library(dynwrap)

library(dynmethods)

library(tidyverse)

models <- infer_trajectories(data, list(ti_slingshot(), ti_monocle3(), ti_paga()))

Output:

Registered S3 methods overwritten by 'zellkonverter':
  method                                             from      
  py_to_r.numpy.ndarray                              reticulate
  py_to_r.pandas.core.arrays.categorical.Categorical reticulate

── Attaching core tidyverse packages ───────────────────────────────────────────────────────────── tidyverse 2.0.0 ──
✔ dplyr     1.1.2     ✔ readr     2.1.4
✔ forcats   1.0.0     ✔ stringr   1.5.0
✔ ggplot2   3.4.3     ✔ tibble    3.2.1
✔ lubridate 1.9.2     ✔ tidyr     1.3.0
✔ purrr     1.0.2     
── Conflicts ─────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors

Error Message:

dynwrap_backend option not set, assuming that you want to run this method as an R wrapper

Skipping install of 'tislingshot' from a github remote, the SHA1 (65248eca) has not changed since last install.
  Use `force = TRUE` to force installation

Error in ti_monocle3(): could not find function "ti_monocle3"
Traceback:

1. infer_trajectories(data, list(ti_slingshot(), ti_monocle3(), 
 .     ti_paga()))

[rcannood]

Hi @akattapuram-insitro !

Thanks for taking the time to file a bug report.

I want to be transparent about the current status of the dynverse project. Unfortunately, due to a lack of funding, the some of the dynverse packages are currently unmaintained. However, I have been considering revitalising this project by bringing some of the code base to the openproblems.bio framework for a more maintainable benchmarking framework.

I'm intrigued by your interest and would be happy to discuss your particular needs. Are you working on performing a evaluation of trajectory inference methods, or are interested in applying trajectory inference methods on your dataset of interest?

Robrecht

[akattapuram-insitro]

Hi! Thanks for your quick reply! I ran a few trajectory packages for a dataset (directly from the package's own tutorials) and was trying to perform evaluations of the different methods between the 5 trajectory packages I chose for comparison. The packages I used were slingshot, paga, monocle3, palantir, and cellrank meets cytotrace. I saw that palantir and cellrank aren't included and was trying to create wrappers for this. If you have any advice for this, it would be super helpful!! Thank you so much!