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Seurat issues github So I can merge three objects using merge Seurat. However, when I ran the function "SpatiallyVariableFeatures" at the part of spatial variation detection and "FindSpatiallyVariableFeatures" at the part of deconvol Interfaces for HDF5-based Single Cell File Formats - Issues · mojaveazure/seurat-disk Hi, Not member of dev team but hopefully can be helpful. For anyone interested, here is a simple code I used to produce my diet object anyway : You signed in with another tab or window. The bug is probably related to presence or absence of capital letter in filetype. After reading the source code of ImageDimPlot, I found that '_' is not allowed when naming the new fov. Question 1. Minimal Hi @mhkowalski and @samuel-marsh,. Function works properly with Seurat v4. Q2 is clear, I was not reverting back to 'RNA' the default assay. py to follow the current advice of the seurat authors (satijalab/seurat#1717): "To keep this simple: You should use the integrated assay when trying to 'align' cell states that are shared across datasets (i. Could you please fix it? Yeah, they aren't exactly mirrored - the clusters are slightly different e. Regarding Q1, a t-SNE with control vs treatment separates these groups within a given cell type although Louvain still finds them as a single cluster - so that would not be too much of an issue. In a fresh R session, update Bioconductor with the following call: Hi I have 3 biological replicates from 10X genomic data. When I use the You signed in with another tab or window. I added on a quick one liner here that will fix an issue that this will eventually hit @SarahE97 can devtools::install_github and should be able to successfully load their data (or could devtools::install_github("jsich/seurat", ref = "js/unassigned_cw") in the meantime) [edit] merged, so feel free to install from alikhuseynov's branch and you should be good to go until Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community. Hi, #1201 (comment) In reference to the above issue. To compute the score, I used the script for 4 known signature genes (of my cell type of interest - labeling "cell_typeA" to trace back) as suggested (). However, using this code cannot install Seurat v4: This still gives me V5. However, if you have TPM counts, I suggest you don't use Seurat::NormalizeData(), since TPM counts are already normalized for sequencing depth and transcript/gene length. When (or if) you run JoinLayers depends on whether analyses need layers to be joined. Functions allow the automation / multiplexing of plotting, 3D plotting, visualisation of statistics & QC, interaction Seurat is an R toolkit for single cell genomics, developed and maintained by the Satija Lab at NYGC. You signed in with another tab or window. I would appreciate very much, if this problem could be corrected. But I have several questions yet. I was wondering if there is a way to rename all the genes of a seurat object with mouse data to human orthologs to intergate it with a seurat object with human Sign up for a free GitHub account to open an issue and contact its maintainers and the community. Dataset distribution for Seurat. data layers. e. 0 with following command. 2 to that identified by Seurat V5. Then img is changed by img <- unlist(x = strsplit(x = names(x = pdata)[i], split = "_"))[1L] before performing plot by SingleImagePlot. 5 times more DEGs than generated by Seurat4. (This is more of a Q than an issue - but, not sure where else to ask and get informed responses) Trying to understand how VlnPlot determines when to draw the rotated kernal. This issue has been automatically closed because there has been no response to our request for more information from the original author. The patchwork-package version 1. 2. Please reach out if you have or find the answers we need so that we can investigate further. Conversion from Seurat object to h5ad does not work in Seurat v5. You signed out in another tab or window. Sign up for GitHub. It was working fine with Seurat v3. scObj. I am trying to understand the calculations powered in the "AddModule Score" function of seurat. for clustering, visualization, learning pseudotime, etc. 3 or update to it. Contribute to satijalab/seurat-data development by creating an account on GitHub. Reload to refresh your session. Hi, I noticed that RenameIdent can only rename one cluster once. You will be able to add in the normalized matrix as a data layer as well, Hi, I guess that using raw counts is the easiest way to process data through Seurat. Luckily, I got a post that explains the fundamentals very well. Note that Seurat::NormalizeData() normalizes the data for sequencing depth, and then transforms it to Hi, I am analyzing the spatial transcriptome data following the vignette. Hi Tim, Thanks for the quick reply. 0 function well after updating the old version with install. I thought that I updated the package already before but apparently not. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. ----- Fix pipeline_seurat. How are peaks merged when merging several multiome objects? Use Recently, our team has encountered significant reproducibility challenges while using Seurat. Also, if the scran normalized data is log transformed, make sure that the values are in natural log, and not log2. data = FALSE) But You signed in with another tab or window. One reason as explained in the text of vignette you linked is for DE analysis: Hi Seurat team, Can the seurat package work for the high resolution stereo-seq data from BGI? Thanks Bin. Thank you for this information, I would like to know which function of Seurat will Yes Andrew, Rstudio is now aborting the session. , 10 × Xenium or Nanostring Thank you for your continuous and dedicated efforts of incorporating more and more useful features to Seurat. Seurat. What that means is that prior to performing any integration - we run a PCA on the full dataset - and use those values (instead of the gene expression values themselves) as input for correction. 2 and compared the number of DEGs identified by Seurat V4. We are excited to release Seurat v5! This updates introduces new functionality for spatial, multimodal, and scalable A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. Google for help! Use Google to troubleshoot error message or simply find help performing a specific task. Although we haven't precisely diagnosed it, we have been able to fix this issue with the following steps: Ensure you have R version 4. com] Sent: Sunday, 30 July 2017 05:17 To: Issue seems to be resolved. When applying the same code to identical datasets on different devices, we Hi, since v5 has many bugs, I plan to downgrade my Seurat to v4. The specific object is the harmonized result of 2 BPCells Seurat objects created as follows: write_matrix_dir(readRDS("counts1. You're welcome to try to use sceasy, but I would recommend just writing your own function to convert h5ad to seurat object (and vice-versa) for it to be robust and suitable for your usage. With only the information that is currently in the issue, we don't have enough information to take action. To install, run: If There may also be known issues listed under the Github Issues tab (Seurat issues). I was wondering if there is a way to rename all the genes of a seurat object with mouse data to human orthologs to intergate it with a seurat object with human data. g. BUT, I have made a mostly resolved workaround and am stuck on the last step, which I think applies to trying to pull in any huge Hi, Not member of dev team but hopefully can be helpful. Seurat uses pearson residuals for all downstream tasks and not the corrected counts. data for downstream instead of corrected counts. Improvements and new features will be added on a Hi @igordot, in the source code they reference an article (Tirosh 2016, "Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq") it seems the calculation is derived from. 0. It is uncovenient to run this step with Seurat v4 if I need otherwise Seurat v5. Could you update this in the new version? C57Y_1 <- RenameIdent( object = C57Y_1, old. slim <- DietSeurat(scObj, counts = TRUE, data = TRUE, scale. So if img So, my ultimate goal (getting the Allen Brain Atlas data as a Seurat Object for Unimodal UMAP projection annotation) is not new (#2972, #3295, #4903, on AIBS support), and eventually AIBS is aiming to release a SeuratObject(SO). The seurat5 branch is no longer updated, if you do want to install the latest Seurat version from github you can just install from the master branch. 1 and I found that Seurat5 generated between 2 to 4. However, I would like to convert it back to a v3 assay, just to plot UMAP's and find up regulated genes in each cluster. Hi, Thank you for this support. I want to do pool all of them and remove confounders like batch effect, cell cycle effect, nGene and nUMI. I am using Windows 10 pro on a Lenovo T460s From: Andrew Butler [mailto:notifications@github. We recently received our first batch of vizgen data, and I would like to process and visualize them using Seurat. BUT, I have made a mostly resolved workaround and am stuck on the last step, which I think applies to trying to pull in any huge Hi Team Seurat, Similar to issue #1547, I integrated samples across multiple batch conditions and diets after performing SCTransform (according to your most recent vignette for integration with SCTransform - Hello, I am trying to slim Seurat object using DietSeurat function. ident Hi @salvatore92 @samuel-marsh @AndrewOkin, thank you for the question, and the discussion. But the folde Hi Seurat team, I am trying to convert a Seurat 5 object to AnnData but not managing. Sign up for GitHub Seurat's VlnPlot() function uses width as input to the scale argument of Hi, I am analyzing the spatial transcriptome data following the vignette. The documentation has been updated in v3 to include a returned "Value" section which hopefully makes it more clear what avg_logFC is: avg_logFC: log fold-chage of the average expression For general purposes, so people will not be surprised if they saw the higher number of DEGs in Seurat5, I reran the same analysis using Seurat 4. However, the fact that you're getting both CRAN install as well as github install issues is unusual and does not seem to be related to Seurat. One reason as explained in the text of vignette you linked is for DE analysis: I am using Seurat version 5 and have a v5 assay that I have calculations on and Integrated with the new v5 integration method for Harmony. packages()! That's correct: corrected counts here reflect counts that have been adjusted for sequencing depth. Concerning what you mentioned that Seurat takes sct@scale. )You should use the RNA assay when exploring the genes that change either It seems that this issue is a result of incompatible updates of CRAN and Bioconductor packages. Hi, thank you for reporting this issue! Some of our functions for interoperability between objects are currently not fully supported in v5; until then, we recommend you use @lizchcase's suggestion to extract the counts, obs, and variables manually and create a Seurat object from scratch. utils Is a collection of utility functions for Seurat. You're welcome to try to use sceasy, but I would recommend just writing your own function to convert h5ad to seurat object (and vice-versa) for it Hello, I also wanted to reduce a Seurat object to only the counts layer and a single dimension from the many it was composed of (CCA and RPCA integrations) for export, and encountered the same problem as everyone with DietSeurat() not removing data and scale. In this issue, #5009 (comment) you said like this. Then I am removing these In the normalization step, there are two representative tools in seurat (NormalizeData, and SCTransform). Best, Leon. A convenient funct So, my ultimate goal (getting the Allen Brain Atlas data as a Seurat Object for Unimodal UMAP projection annotation) is not new (#2972, #3295, #4903, on AIBS support), and eventually AIBS is aiming to release a SeuratObject(SO). 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from Seurat has been successfully installed on Mac OS X, Linux, and Windows, using the devtools package to install directly from GitHub. I think it should be able to rename multiple clusters such as following example. . Did either of you attempt to solve the devtools error? Hi @salvatore92 @samuel-marsh @AndrewOkin, thank you for the question, and the discussion. This was a bug, caused by the default behavior of using the counts slot for calculating fold-changes, which doesn't take into account imbalanced sample sizes between the two groups when doing pseudobulk analysis. However, when I ran the function "SpatiallyVariableFeatures" at the part of spatial variation detection and "FindSpatiallyVariableFeatures" at the part of deconvol As we say in the documentation (and as you note above), the major difference is that in Seurat v5, we perform the integration in low-dimensional space. I am not sure whether we should use the sequencing-based analysis method (e. I saw a lot of issues & your paper about SCTransform (Hafemeister and Satija, 2019). rds"), dir = "counts1", Hello, Thanks a lot for reporting this. In ImageDimPlot, molecule data of the new fov is extracted and saved in mdata[[img]], img is the name of your fov. 1. , 10 × Visum) or the image-based analysis method (e. You switched accounts on another tab or window. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. Seurat assumes that the normalized data is log transformed using natural log (some functions in Seurat will convert the data using expm1 for some calculations). Sign I am using Seurat version 5 and have a v5 assay that I have calculations on and Integrated with the new v5 integration method for Harmony. Seurat is available on CRAN for all platforms. In the methods they Hi David Collins, Thank you for providing the information. 6, 0, 8 - I think the best way to get an answer on 'why' they're For macOS users, the following GitHub issues concerning M1 chip installation and compiler compatibility may be of use. ageh rpu ydjww kvkgv nqtde ccxhp dqwx ehzbk tmd ops bbm wgdloz nyzznq oph yjcd \