seurat | scene simplification technology designed to process

by googlevr C++ Version: Current License: Apache-2.0

X-Ray Key Features Code Snippets Community Discussions(10)Vulnerabilities Install Support

kandi X-RAY | seurat Summary

seurat is a C++ library. seurat has no bugs, it has no vulnerabilities, it has a Permissive License and it has medium support. You can download it from GitHub.

The root node is a Capture object. Matrices are in row-major order.

Support

Quality

Security

License

Reuse

Support

seurat has a medium active ecosystem.

It has 851 star(s) with 96 fork(s). There are 82 watchers for this library.

It had no major release in the last 6 months.

There are 27 open issues and 7 have been closed. On average issues are closed in 13 days. There are 1 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of seurat is current.

Quality

seurat has no bugs reported.

Security

seurat has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

License

seurat is licensed under the Apache-2.0 License. This license is Permissive.

Permissive licenses have the least restrictions, and you can use them in most projects.

Reuse

seurat releases are not available. You will need to build from source code and install.

Installation instructions are not available. Examples and code snippets are available.

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seurat Key Features

No Key Features are available at this moment for seurat.

seurat Examples and Code Snippets

No Code Snippets are available at this moment for seurat.

Community Discussions

Trending Discussions on seurat

Error in make.unique: 'names' must be a character vector when switching tabsetPanel in shiny

How to interpret decimal values for nCount_RNA in Seurat Object

Extract names of genes expressed by at least 10% of cells in a cluster

R: Symbol not found: _libintl_dgettext

R convert data into a vector

Cholmod error 'out of memory' : Merging Seurat Objects

Changing the legend in complex heatmap

using purrr::map to rename row names in elements within lists in a bigger list?

Transform dataframe data in R

Using OpenEXR with Bazel?

QUESTION

Error in make.unique: 'names' must be a character vector when switching tabsetPanel in shiny

Asked 2021-Jun-02 at 13:20

In the example below I get following error many times printed when switching back and forth between radio buttons iris and About-

...

ANSWER

Answered 2021-Jun-02 at 13:20

The error was coming from the esquisse package unfortunately (https://github.com/dreamRs/esquisse/issues/164). It has been resolved now by the developer.

And second part of my question was answered by @bretauv. Thank you again!

Source https://stackoverflow.com/questions/67535034

QUESTION

How to interpret decimal values for nCount_RNA in Seurat Object

Asked 2021-Apr-14 at 18:05

My dataset is very strange. When I create the Seurat object and load the metadata for it, all of the values in the nCount_RNA are decimal values instead of integers. How should I interpret this? Is there an issue with the data itself or something I can do to work around this? I ask because later on in my analysis, the functions can't seem to find the nCount_RNA object, and I believe the decimal values are the reason why.

Metadata for Seurat Object

Here is the code I used to create this object:

...

ANSWER

Answered 2021-Apr-14 at 18:05

The file you read in, it is normalized somehow, and is definitely not the count data:

Source https://stackoverflow.com/questions/66620204

QUESTION

Extract names of genes expressed by at least 10% of cells in a cluster

Asked 2021-Mar-27 at 00:50

I have a Seurat object with defined clusters. I need to extract a list of all genes that are expressed by at least 10% of cells in my cluster. I need to repeat it for every cluster that I have, separately.

I know one code that could potentially extract genes expressed by at least 10% of cells from the whole Seurat:

...

ANSWER

Answered 2021-Mar-27 at 00:50

You could use lapply to iterate over the factor levels of your clusters to subset and filter them individually and use setNames to name the resulting list. Below is a reproducible example:

Source https://stackoverflow.com/questions/66824012

QUESTION

R: Symbol not found: _libintl_dgettext

Asked 2021-Mar-24 at 13:01

I am running R in OSX Mojave and am getting a following error when loading any packages with mgcv dependency;

...

ANSWER

Answered 2021-Mar-24 at 13:01

updating to the latest Brew version of r 4.0.4_2 and getting rid of /Library/Frameworks/R.framework cured it.

Source https://stackoverflow.com/questions/66694970

QUESTION

R convert data into a vector

Asked 2021-Feb-23 at 17:02

I have an object (Seurat object) an I need to get certain data out of it

...

ANSWER

Answered 2021-Feb-23 at 17:02

Solved it! I'm pretty disappointed by myself, because I didn't know this function existed:

Source https://stackoverflow.com/questions/66335127

QUESTION

Cholmod error 'out of memory' : Merging Seurat Objects

Asked 2021-Feb-06 at 23:16

I am trying to merge Seurat class objects that contain transcriptome count data (sparse matrix). I am relatively new to R, so any help/solutions is appreciated. I have added a screenshot of the data I'm working with.

...

ANSWER

Answered 2021-Feb-06 at 23:16

The machine used to process the data in the original question has a 64-bit Windows operating system running a 32-bit version of R. The result from memory.size() shows that approximately 2.4Gb of RAM is available to the malloc() function used by R. The 32-bit version of R on Windows can access a maximum of slightly less than 4Gb of RAM when running on 64-bit Windows, per the help for memory.size().

Memory Limits in R tells us that in 32-bit R on Windows it is usually not possible to allocate a single vector of 2Gb in size due to the fact that windows consumes some memory in the middle of the 2 Gb address space.

Once we load the data from the question, the zfbrainList object consumes about 1.2Gb of RAM.

Source https://stackoverflow.com/questions/66079047

QUESTION

Changing the legend in complex heatmap

Asked 2021-Jan-10 at 21:30

With this code I have this complexheatmap

...

ANSWER

Answered 2021-Jan-10 at 21:30

Heatmap(mat, border = T, show_column_names = F,
        rect_gp = gpar(col = "white", lwd = 1),
        column_split = response$response, 
        col = c("-2" = "blue", "0" = "grey", "1" = "red"),
        heatmap_legend_param = list(at = c("-2", "0", "1"), labels = c("Del", "Netral", "Amp")),
        show_column_dend = F,
        show_row_dend = F,
        left_annotation = left_annotation,
        right_annotation = right_annotation,name = "CNV",
        row_names_gp = gpar("fontface" = "italic")
)

Source https://stackoverflow.com/questions/65657662

QUESTION

using purrr::map to rename row names in elements within lists in a bigger list?

Asked 2020-Dec-01 at 14:25

{library(Seurat)
library(tidyverse)
library(purrr)}



dirNames <- unique(dirname(list.files("data/scRNA_CITE",
                          full.names = T,
                          recursive = T)))


######


#reading multiple directories and a resultant list
dat <- purrr::map(dirNames, Read10X)
names(dat) <- dirNames

#reading just one file
#M06 <- Read10X(data.dir = "data/m06/filtered_feature_bc_matrix/")

#renaming the rows of a list element (here named antibody capture) within one list works! 
rownames(x = M06[["Antibody Capture"]]) <- gsub(pattern = "*_TotalSeqC", replacement = "", 
                                                x = rownames(x = M06[["Antibody Capture"]]))

#creating function for purrr
change_rname <- function(x){
  rownames(x[["Antibody Capture"]]) <- sub(pattern = "*_TotalSeqC", replacement = "", x[["Antibody Capture"]])
}

  
 # using the same function to rename multiple elements within multiple lists of a bigger list works temporarily BUT DOES not get saved within the bigger list
purrr::map(dat,
           ~change_rname(.x))

...

ANSWER

Answered 2020-Dec-01 at 14:25

Return the changed dataframe from the function.

Source https://stackoverflow.com/questions/65091524

QUESTION

Transform dataframe data in R

Asked 2020-Oct-23 at 20:08

I have a dataframe in R of data look likes this:

and I want to transform the table to this

What is the fastest way to do it in R?

Here is how I did it, but I admit that it's very long

...

ANSWER

Answered 2020-Oct-23 at 19:59

We can use pivot_longer

Source https://stackoverflow.com/questions/64506529

QUESTION

Using OpenEXR with Bazel?

Asked 2020-Oct-04 at 19:17

I want to use OpenEXR in a Bazel project.

My WORKSPACE.bazel look like this:

...

ANSWER

Answered 2020-Oct-04 at 19:17

In the meantime, I was able to solve the problem. Base on the BUILD file file from seurat I took an up to date master version von OpenEXR and started to fix all issues. The final BUILD.bazel was tested successfully with Ubuntu 16.08 GCC, LLVM and Windows 10 VS2019.

I created my own bazel branch for the OpenEXR: https://github.com/Vertexwahn/openexr/tree/bazel

Source https://stackoverflow.com/questions/64089675

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install seurat

You can download it from GitHub.

Support

For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .

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