Greenleaflab/archr

Author: mhlu

August undefined, 2024

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 … WebMay 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 …

GreenleafLab/ArchR: Analyzing single-cell regulatory chromatin in …

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. WebArchR: An integrative and scalable software package for single-cell chromatin accessibility analysis (Granja JM*, Corces MR*, et al. 2024) Link : … css style for dropdownlist

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

WebMay 23, 2024 · GreenleafLab / ArchR Public. Notifications Fork 95; Star 282. Code; Issues 15; Pull requests 9; Discussions; Actions; Projects 0; Security; Insights ... Other … WebNov 10, 2024 · GreenleafLab / ArchR Public. Notifications Fork 96; Star 284. Code; Issues 15; Pull requests 9; Discussions; Actions; Projects 0; Security; Insights New issue Have a question about this project? ... ArchR logging to : ArchRLogs/ArchR-addReproduciblePeakSet-a325acb7b94-Date-2024-11-10_Time-17-01-14.log If there is … WebOct 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 … early 1990s disney shows

Tutorial ArrowFiles Error · Issue #1071 · GreenleafLab/ArchR

implementation of seurat DotPlot function · GreenleafLab ArchR ...

Web5 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 … WebThis is an automated email from the git hooks/post-receive script. rekado pushed a commit to branch master in repository guix. The following commit(s) were added to ... css style for imagesWebOct 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 … early 1980\\u0027s map of alston mass

"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 . " - Greenleaflab/archr

Greenleaflab/archr

ArchR is running safely in R CLI, but "Cairo is not …

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. 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.

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

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. WebOct 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 …

WebGreenleafLab / ArchR Public. Notifications Fork 95; Star 282. Code; Issues 15; Pull requests 9; Discussions; Actions; Projects 0; Security; Insights Getting tile matrix ... I … 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'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.

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... css style for fontWebI 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... css style hierarchyWebJun 14, 2024 · GreenleafLab / ArchR Public Notifications Fork 95 Star 282 Code Issues 15 Pull requests 9 Discussions Actions Projects Security Insights Peak call summary #821 Unanswered NoemieL asked this question in Questions / Documentation edited by rcorces NoemieL on Jun 14, 2024 Hello, css style for formWebSep 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. early 1990s vs late 1990sWebOptions include "Macs2" for using macs2 callpeak or "Tiles" for using a TileMatrix. #' @param reproducibility A string that indicates how peak reproducibility should be … css style for text colorWeb4 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... css style for p tagWebJul 12, 2024 · GreenleafLab / ArchR Public Notifications Fork 95 Star 281 Code Issues 15 Pull requests 9 Discussions Actions Projects Security Insights implementation of seurat … early 1980\u0027s map of alston mass