Greenleaflab/archr
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 … 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.
Greenleaflab/archr
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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 … 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 …
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... Web5 hours ago · GreenleafLab / ArchR Public. Notifications Fork 96; Star 284. Code; Issues 18; Pull requests 9; Discussions; Actions; Projects 0; Security; Insights ... , reducedDims …
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 … WebMar 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.
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.
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 … fix your shirt your gun showingWebArchR 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. cannondale slate road bicycleWebMay 27, 2024 · GreenleafLab / ArchR Public. Notifications Fork 95; Star 282. Code; Issues 15; Pull requests 9; Discussions; Actions; Projects 0; Security; Insights New issue Have … fix your shitWebArchR: An integrative and scalable software package for single-cell chromatin accessibility analysis (Granja JM*, Corces MR*, et al. 2024) Link : … cannondale slice triathlon bikeWebGreenleafLab / ArchR Public. Notifications Fork 95; Star 282. Code; Issues 15; Pull requests 9; Discussions; Actions; Projects 0; Security; Insights Getting tile matrix ... I have generated archR project and generated tile matrix, and also extracted the matrix using getMatrixFromProject() however it is saved as an R object and can not figure ... fix your screen with toothpasteWebJan 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 … fix your scheduleWebAug 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 fix your screen near me