Greenleaflab/archr

Author: wjcx

August undefined, 2024

WebJul 12, 2024 · GreenleafLab / ArchR Public Notifications Fork 95 Star 281 Code Issues 15 Pull requests 9 Discussions Actions Projects Security Insights implementation of seurat … Web5 hours ago · GreenleafLab / ArchR Public. Notifications Fork 96; Star 284. Code; Issues 18; Pull requests 9; Discussions; Actions; Projects 0; Security; Insights ... , reducedDims …

Peak call summary · GreenleafLab ArchR · Discussion #821

WebHello, I copy the ArchR output to another computer, while plotEmbedding function does not work due to the working directory sorted in ArchR object. 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. can t come up with a business idea

ArchR object as Signac object · Issue #349 · GreenleafLab/ArchR

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 … WebJun 6, 2024 · GreenleafLab / ArchR Public. Notifications Fork 95; Star 282. Code; Issues 15; Pull requests 9; Discussions; Actions; Projects 0; Security; Insights; Getting … 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 … can t concentrate awork after breakup

ArchR will not install · Issue #563 · GreenleafLab/ArchR · GitHub

getMarkerFeatures() Error in nabor::knn(data = data, …

WebApr 30, 2024 · Previously, I have used ArchR successfully to analyze fragments.tsv.gz files from cellranger-atac outputs. However, I tried to filter out specific cell barcodes in the … WebJan 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 … can t con an honest johnWebOct 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 … flashback.se forum

"WebJan 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... " - Greenleaflab/archr

Greenleaflab/archr

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

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 … WebOct 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 …

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WebAug 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. 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.

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 identify the cell type in each cluster? (without scRNA-Seq data) Full tutorial looks not show the method how to. Just suggested to combine with scRNA-Seq data. WebAug 10, 2024 · GreenleafLab / ArchR Public Notifications Fork 93 Star 279 Code Issues 15 Pull requests 9 Discussions Actions Projects Security Insights New issue Error in H5Fopen (file): HDF5. File accessibilty. Unable to open file #972 Closed brianpenghe opened this issue on Aug 10, 2024 · 9 comments brianpenghe commented on Aug 10, 2024 completed

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 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.

WebI think I safely installed ArchR, and confimed that ArchR is running safely in R command line. But when I run the ArchR package in rstudio, "WARNING : Cairo check shows Cairo is not functional. ggp...

WebNov 30, 2024 · Extract peaks from each subsetted ArchR projects as .bed file. Subset for each cell type. Call peaks on subsetted dataset with Macs2. Extract peaks from each … flashbacks effect on readerWebOptions include "Macs2" for using macs2 callpeak or "Tiles" for using a TileMatrix. #' @param reproducibility A string that indicates how peak reproducibility should be … flashback segaWebI think I safely installed ArchR, and confimed that ArchR is running safely in R command line. But when I run the ArchR package in rstudio, "WARNING : Cairo check shows … can t concentrate on anything depressionWebGreenleafLab / ArchR Public. Notifications Fork 95; Star 282. Code; Issues 15; Pull requests 9; Discussions; Actions; Projects 0; Security; Insights Getting tile matrix ... I … flashback semi acousticWebMar 2, 2024 · Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community. can t complainWebMay 23, 2024 · GreenleafLab / ArchR Public. Notifications Fork 95; Star 282. Code; Issues 15; Pull requests 9; Discussions; Actions; Projects 0; Security; Insights ... Other … flashback sentenceWebArchR 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 … can t connect oneplus 5 to pc