Greenleaflab/archr

Author: dkph

August undefined, 2024

WebGreenleafLab / ArchR Public. Notifications Fork 95; Star 282. Code; Issues 15; Pull requests 9; Discussions; Actions; Projects 0; Security; Insights Getting tile matrix ... I … WebGreenleafLab / ArchR Public Notifications Fork 93 274 Actions Projects Error in H5Fopen (file): Unable to open HDF5 file when using subsetArchRProject to create new arrow files JohnGenome opened this issue on Jul 16, 2024 · 26 comments JohnGenome commented on Jul 16, 2024

I would like to run cellchat on my Paired scATAC-seq and scRNA …

WebJun 6, 2024 · GreenleafLab / ArchR Public. Notifications Fork 95; Star 282. Code; Issues 15; Pull requests 9; Discussions; Actions; Projects 0; Security; Insights; Getting … WebJan 30, 2024 · ArchR has a built-in logging functionality for all complex functions. You MUST attach your log file (indicated in the console output) to this issue. Just drag and … dysphagia mechanical soft diet handout

createArrowFiles Error · Issue #727 · GreenleafLab/ArchR - GitHub

WebJul 5, 2024 · Version. 1.0.2. Package repository. View on GitHub. Installation. Install the latest version of this package by entering the following in R: install.packages ("remotes") … WebArchR logging to : ArchRLogs/ArchR-addGeneIntegrationMatrix-11f6561f7d62-Date-2024-09-29_Time-12-16-33.log If there is an issue, please report to github with logFile! 2024-09-29 12:16:33 : Running Seurat's Integration Stuart* et al 2024, 0.002 mins elapsed. WebLove Archr. I went through the entire pipeline with my multiome paired scRNAseq and ATACseq data on 11 different samples. Now I have clusters and UMAPs generated via LSI-combined and harmony and I would like to run cellchat on them. But I have no idea how to extract the RNAseq seurat object from my Archr Project. c sets

copy ArchR outputs to another computer, how to change …

Error during doublet scoring · Issue #218 · GreenleafLab/ArchR

Web4 hours ago · I noticed that when I used the getMatrixFromProject function, there was a problem about HDF5. The following is the detailed related content: Attach your log file ArchR-getMatrixFromProject-1bfab75719cfea-Date-2024-04-14_Time-05-37-50.log... WebArchR is a full-featured R package for processing and analyzing single-cell ATAC-seq data. ArchR provides the most extensive suite of scATAC-seq analysis tools of any software … dysphagia mechanical softWebAug 13, 2024 · Hello, I am trying to export the peaks by cells accessibility matrix for external use, but when I use getMatrixFromProject the number of cells is much fewer than the number of cells in my ArchR project. I used the following code to call peaks and extract the matrix, and I included the log file for my getMatrixFromProject call. cset schools bristol

"WebMay 23, 2024 · GreenleafLab / ArchR Public. Notifications Fork 95; Star 282. Code; Issues 15; Pull requests 9; Discussions; Actions; Projects 0; Security; Insights ... Other … " - Greenleaflab/archr

Greenleaflab/archr

WebMay 25, 2024 · GreenleafLab / ArchR Public Notifications Fork 93 Star 276 Code Issues 15 Pull requests 9 Discussions Actions Projects Security Insights New issue addGeneIntegrationMatrix error #174 Closed Brawni opened this issue on May 25, 2024 · 8 comments Brawni commented on May 25, 2024 • edited WebJul 20, 2024 · ArchR logging to : ArchRLogs/ArchR-getMarkerFeatures-c733ad6d8bf-Date-2024-01-04_Time-05-28-14.log If there is an issue, please report to github with logFile! 2024-01-04 05:28:14 : Matching Known Biases, 0.001 mins elapsed.

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WebI'm continuously try to set-up and understand the data analysis workflow using ArchR. During following "full tutorial", I got question. After calculating gene scores, how can I … WebJul 27, 2024 · Yes - ArchR works for ATAC and RNA data acquired from different cells (see the manual) as well as the newer multiome approaches. Our expectation is that you …

WebOct 17, 2024 · GreenleafLab / ArchR Public Notifications Fork 95 Star 282 Code Issues 16 Pull requests 9 Discussions Actions Projects Security Insights New issue ArchR object … WebJul 27, 2024 · Yes - ArchR works for ATAC and RNA data acquired from different cells (see the manual) as well as the newer multiome approaches. Our expectation is that you process your RNA-only data outside of ArchR (for ex. with Seurat) and then use that object as import to ArchR. 1 0 replies Sign up for free to join this conversation on GitHub .

WebJun 19, 2024 · Originally I thought there is something wrong with the dataset, but my PI's code works, and at the same time, the ArchR code works fine on the Tutorial dataset under current Conda environment. By the way, I used ArchR in Conda environment on HPC. The following is the sessionInfo(). Maybe, I should make a new ArchR only Conda … WebJul 4, 2024 · ArchR is currently in Beta and will be in active development through the peer review process. ArchR is a full-featured R package for processing and analyzing single … Secure platform, secure data We’re constantly improving our security, audit, … Actions - GitHub - GreenleafLab/ArchR: ArchR : Analysis of Regulatory … We would like to show you a description here but the site won’t allow us. Pull requests 7 - GitHub - GreenleafLab/ArchR: ArchR : Analysis … Explore the GitHub Discussions forum for GreenleafLab ArchR. Discuss code, ask … GitHub is where people build software. More than 83 million people use GitHub … We would like to show you a description here but the site won’t allow us.

Web4 hours ago · I noticed that when I used the getMatrixFromProject function, there was a problem about HDF5. The following is the detailed related content: Attach your log file …

Web5 hours ago · GreenleafLab / ArchR Public. Notifications Fork 96; Star 284. Code; Issues 18; Pull requests 9; Discussions; Actions; Projects 0; Security; Insights ... , reducedDims … dysphagia mechanically altered level 2 dietWebJan 14, 2024 · ArchR-addDeviationsMatrix-1788a61a09cea-Date-2024-01-14_Time-17-53-59.log Hi I generated some subclusters through the subsetArchRProject() command and saved them, and then some subclusters will hav... dysphagia obstructionWebOct 11, 2024 · ArchR-createArrows-6dde1096a29b-Date-2024-10-11_Time-13-52-12.log Hello, I am trying to run through the tutorial data set and have run into an error where … dysphagia mechanical soft diet recipesWebOct 14, 2024 · #' @param db A string indicating the database or a path to a database to use for peak annotation. Options include ArchR, #' LOLA, and a valid path to a file of class … dysphagia nutrition and hydration post strokeWebMar 4, 2024 · Describe the bug I am unable to get exactly the same Arrow files when using BAM and fragment file inputs from the same data set. For example, using the possorted_bam output from 10x and the fragments.tsv.gz output from 10x give different pass-filter cells and different fragment counts. dysphagia mech soft dietWebJan 16, 2024 · In the creation of pseudobulk replicates, it can happen in a sample-aware manner, which is great. However, it seems like in certain cases where minCells per … cset science testing resourcesWebAug 13, 2024 · Hello, I am trying to export the peaks by cells accessibility matrix for external use, but when I use getMatrixFromProject the number of cells is much fewer than the … cset science 215 study guide