Greenleaflab/archr

WebOptions include "Macs2" for using macs2 callpeak or "Tiles" for using a TileMatrix. #' @param reproducibility A string that indicates how peak reproducibility should be … 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 …

Getting PeakMatrix with getMatrixFromProject() · GreenleafLab …

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 … WebSep 28, 2024 · I am using my dataset for ArchR analyses. These are scATAC seq dataset. I am able to run through the initial steps of creation of arrow files but it seems to be stuck at "Creating ArrowFile From Temporary File 9.113 mins elapsed" for over two hours. small glass cooking dish https://aminolifeinc.com

Unable to incorporate "ENCODETFBS" using addArchRAnnotations …

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 … 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 … 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... songs with gonna in the title

Cell type identification without scRNA-Seq data. · GreenleafLab ArchR ...

Category:Tutorial ArrowFiles Error · Issue #1071 · GreenleafLab/ArchR

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Greenleaflab/archr

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

WebMar 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. 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.

Greenleaflab/archr

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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... 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

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. 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 ...

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 … WebHello, I copy the ArchR output to another computer, while plotEmbedding function does not work due to the working directory sorted in ArchR object.

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 … songs with gone in the titleWeb5 hours ago · GreenleafLab / ArchR Public. Notifications Fork 96; Star 284. Code; Issues 18; Pull requests 9; Discussions; Actions; Projects 0; Security; Insights ... , reducedDims = "IterativeLSI" ) ArchR logging to : ArchRLogs/ArchR-addPeak2GeneLinks-28e376a2da62-Date-2024-04-14_Time-16-57-19.log If there is an issue, please report to github with … songs with good beat dropsWebGreenleafLab / ArchR Public. Notifications Fork 95; Star 282. Code; Issues 15; Pull requests 9; Discussions; Actions; Projects 0; Security; Insights Getting tile matrix ... I … small glass containers with lids wholesaleWebJul 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. small glass corner computer deskWebOct 5, 2024 · ArchR logging to : ArchRLogs/ArchR-getMarkerFeatures-ea792557637e-Date-2024-09-15_Time-19-21-01.log If there is an issue, please report to github with logFile! 2024-09-15 19:21:02 : Matching … songs with good beatsWebJan 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 … small glass corked bottlesWebJul 12, 2024 · GreenleafLab / ArchR Public Notifications Fork 95 Star 281 Code Issues 15 Pull requests 9 Discussions Actions Projects Security Insights implementation of seurat … songs with good figurative language