Ramon Massoni-Badosa

Problem with selectFeatures

5

Dear scmap team, I am trying to project my scRNA-seq dataset against the Tabula Muris droplet-based reference (which I download from [here](https://github.com/czbiohub/tabula-muris-vignettes/tree/master/data)). This is my code ```{r} # Load the...

control border thickness of Stacked_VlnPlot

8

Hi @samuel-marsh! Thanks for this useful package. Is there anyway to change the border thickness of `Stacked_VlnPlot`? When I save it with ggsave and arrange it into a figure it...

Error addGCBias: trying to load regions beyond the boundaries of non-circular sequence "chr13"

1

Hi, Thanks for developing this wonderful package. I am running chromVAR on my bulk ATAC-seq data. After running the following code chunk: ``` fragment_counts sessionInfo() R version 4.3.2 (2023-10-31) Platform:...

make Human Cell Atlas datasets installable

1

Hi Aaron, I'm currently creating an atlas of all cell types and states in a secondary lymphoid organ in the context of the Human Cell Atlas. As part of the...

Dear PAGA team, Thanks for developing this tool, it's been very useful for my research! I would like to kindly ask you two questions I have regarding its usage. First,...

Problem installing cicero in CentOS 7.9

1

Hi, Thanks for developing this package. I'm trying to install cicero in our CentOS 7.9 cluster, running R 4.3.1. I execute the following command: ``` remotes::[install_github](https://remotes.r-lib.org/reference/install_github.html)("cole-trapnell-lab/cicero-release", ref = "monocle3") ```...

Cargo, the Rust package manager, is not installed or is not on PATH.

7

Hi pycisTopic team, Thanks for developing this package. I'm trying to install it following the [installation guide](https://pycistopic.readthedocs.io/en/latest/installation.html) as follows: ``` git clone https://github.com/aertslab/pycisTopic.git cd pycisTopic pip install -e . ```...

Add pycisTopic images to DockerHub

1

Hi all, Thanks for this wonderful tool! We're trying hard to install pycistopic using pip in our cluster (NYGC), but we keep hitting all sorts of errors. We managed to...