Greenleaflab/archr
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 … 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 …
Greenleaflab/archr
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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. WebGreenleafLab / 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 ...
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 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...
WebFeb 1, 2024 · If I leave out the pal option, the UMAP is plotted correctly in default colors. I have this issue with two different ArchR projects but I have not tried reproducing with 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 …
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 .
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 … cities near sherman txWebOct 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 … cities near shelton ctWebI'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. diary of a wimpy book orderWebApr 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 … cities near silver springs flWebNov 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 … cities near shipshewana inWebJul 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 … cities near sikeston moWebJun 6, 2024 · GreenleafLab / ArchR Public. Notifications Fork 95; Star 282. Code; Issues 15; Pull requests 9; Discussions; Actions; Projects 0; Security; Insights; Getting … cities near shippensburg pa