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trajectory inference
Hello
Is it possible to run trajectory inference of Asc-seurat with R program created (not Asc-seurat created) rds files?
How long can I expect to finish inference for large integrated ads files?
Thanks
GreyRock
Error: Max dimension too large: objects 1, 2 contain fewer than 30 cells. Please specify a maximum dimensions that is less than the number of cells in any object (3).
Hi I am trying to load multple datasets to asc-seurat but I am unable to form the integration object due to the following error.
Max dimension too large: objects 1, 2 contain fewer than 30 cells.
Please specify a maximum dimensions that is less than the number of cells in any object (3).
I will appreciate any assistance : My parameters are
Download trajectory object
Sorry for a second question. Is it possible to export also the R object together with the plots? I would like to know which cells are in the different parts of the trajectory.
Thanks.
data folder
Hi Wendel,
I am eager to try Asc-Seurat but I cannot figure out where the data folder is located on my computer :(.
Can you help?
How to load seurat object .rds file?
Dear
I tried to use asc-seurat. It is smart tool to handle single cell data very easily!
I would like to run asc-seurat with seurat object data that has already been preprocessed, demultiplexed with BD sample tags, and performed dimentionally reduction and clustering analysis in other pipelines.
How can I load this data to asc-seurat pipeline?
Best regards,
Hiroyasu
Error: non-finite entries the input matrix.
Hello.
I am RUNing a Docker container of Asc Seurat.
When I try to run the sample data, I get an error.
I have not changed any values in the GUI.
The place where the error occurs is in the clustering analysis.
I get the message "Error: non-finite entries the input matrix."
Then I noticed that the standard deviation value of the Elbow plot in PCA was wrong.
From the bottom, the values are -1.132312e+240, 5.095405e+240, 1.132312e+241...
I then tried to RUN the container on another server, but the error may or may not occur.
It seems that the error always occurs on a specific host.
Is there any way to determine the cause of this error?
docker build error ERROR: failed to solve: process "/bin/bash -c apt-get update && apt-get install -y xml2 libxml2-dev libssl-dev && apt-get clean" did not complete successfully: exit code: 100
My aim is to build the image from the source code. I don't see any special instructions for building the image so I tried doing it with the docker build command, and the most recent commit without changing anything. On multiple branches.
When I run:
docker build -t single-cell .
or
docker image build -t single-cell .
In the project root where the Dockerfile is
.
├── Dockerfile
├── LICENSE
├── R
├── README.md
├── configuration_file_for_integration_analysis.csv
├── docs
├── global.R
├── scripts
├── server.R
├── sh-bin
├── ui.R
└── www
I get the following error
[+] Building 12.7s (9/83)
=> [internal] load .dockerignore 0.0s
=> => transferring context: 2B 0.0s
=> [internal] load build definition from Dockerfile 0.0s
=> => transferring dockerfile: 3.93kB 0.0s
=> [internal] load metadata for docker.io/kirstlab/asc_seurat:dynverse_v2.2 0.6s
=> [internal] load build context 0.0s
=> => transferring context: 1.82kB 0.0s
=> [ 1/79] FROM docker.io/kirstlab/asc_seurat:dynverse_v2.2@sha256:c927953f47475c8a674eec97d27d5d39627ce3888262b212a62a3279646c39a3 0.0s
=> CACHED [ 2/79] WORKDIR /app 0.0s
=> CACHED [ 3/79] COPY www /app/www 0.0s
=> CACHED [ 4/79] COPY R /app/R 0.0s
=> ERROR [ 5/79] RUN apt-get update && apt-get install -y xml2 libxml2-dev libssl-dev && apt-get clean 12.1s
------
> [ 5/79] RUN apt-get update && apt-get install -y xml2 libxml2-dev libssl-dev && apt-get clean:
#0 0.623 Get:2 http://deb.debian.org/debian testing InRelease [167 kB]
#0 0.866 Get:1 http://cdn-fastly.deb.debian.org/debian sid InRelease [199 kB]
#0 3.119 Get:3 http://cdn-fastly.deb.debian.org/debian sid/main amd64 Packages.diff/Index [63.6 kB]
#0 3.128 Ign:3 http://cdn-fastly.deb.debian.org/debian sid/main amd64 Packages.diff/Index
#0 3.233 Get:4 http://cdn-fastly.deb.debian.org/debian sid/main amd64 Packages [9,565 kB]
#0 7.741 Reading package lists...
#0 12.08 E: Repository 'http://deb.debian.org/debian testing InRelease' changed its 'Codename' value from 'bookworm' to 'trixie'
------
Dockerfile:13
--------------------
11 | COPY R /app/R
12 |
13 | >>> RUN apt-get update && apt-get install -y xml2 libxml2-dev libssl-dev && apt-get clean
14 | RUN apt-get install -y libcurl4-openssl-dev unixodbc-dev && apt-get clean
15 | RUN apt-get install -y gfortran
--------------------
ERROR: failed to solve: process "/bin/bash -c apt-get update && apt-get install -y xml2 libxml2-dev libssl-dev && apt-get clean" did not complete successfully: exit code: 100
I will be working to fix this bug. If someone has encountered the same thing of found a solution we can work together using this thread.
Thanks!
D.E. genes between integrated samples
Never mind
Problem with Select the file window in Trajectory inference tab
Hello.
I've been having some issues with loading the object for a trajectory analysis. When I click on it only a white line comes up instead of the list of files in my RDS folder.
I tried using different browser but it does not seem to change.
Thanks in advance for your help.
Alessandra
problem with heatmap of the trajectory and marker plots
Thank you so much for the nice tool. I'm having problems with the generation of the markers heatmap and the visualization of genes in the trajectory. The message below (the purple one int he right corner) says generating heatmap but the screen becomes dull and the heatmap doesn't appear. I have no problem at all with the generation of the trajectory. Any suggestions?
thank you in advance
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