DESeq2 | Differential gene expression analysis

by mikelove R Version: Current License: No License

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

kandi X-RAY | DESeq2 Summary

DESeq2 is a R library. DESeq2 has no bugs, it has no vulnerabilities and it has low support. You can download it from GitHub.

Differential gene expression analysis based on the negative binomial distribution

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Support

DESeq2 has a low active ecosystem.

It has 265 star(s) with 81 fork(s). There are 22 watchers for this library.

It had no major release in the last 6 months.

There are 3 open issues and 53 have been closed. On average issues are closed in 7 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of DESeq2 is current.

Quality

DESeq2 has 0 bugs and 0 code smells.

Security

DESeq2 has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

DESeq2 code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

DESeq2 does not have a standard license declared.

Check the repository for any license declaration and review the terms closely.

Without a license, all rights are reserved, and you cannot use the library in your applications.

Reuse

DESeq2 releases are not available. You will need to build from source code and install.

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DESeq2 Key Features

No Key Features are available at this moment for DESeq2.

DESeq2 Examples and Code Snippets

No Code Snippets are available at this moment for DESeq2.

Community Discussions

Trending Discussions on DESeq2

Loop through columns to generate PCA from DESeq2 data

Problems in plotting line and error bars on the plot in R

DESEQ2: varianceStabilizingTransformation Error: every gene contains at least one zero, cannot compute log geometric means

Error in DESeqDataSet(se, design = design, ignoreRank) : counts matrix should be numeric, currently it has mode: logical

DESeq2 DDS filter error message using Dplyr

How to solve 'log2FoldChange is not numeric error' on R package EnhancedVolcano?

Running DESeq2 from rpy2

magrittr pipe to righthand side in braces gives error

Cannot specify input dataset in shiny dashboard

Snakemake with R script, error: snakemake object not found

QUESTION

Loop through columns to generate PCA from DESeq2 data

Asked 2022-Mar-09 at 18:08

I'd like to generate a PCA of my bulk RNAseq data, coloured by each of my variables in the DESeq2 object "vsd". My current code looks like this (to generate a single plot):

...

ANSWER

Answered 2022-Mar-09 at 18:08

Let's mock up some data, since the example you provide is too short and ill-formatted to do anything with. I'm assuming you have data of roughly the following structure:

Source https://stackoverflow.com/questions/71411281

QUESTION

Problems in plotting line and error bars on the plot in R

Asked 2021-Oct-11 at 02:50

I have this piece of R code that should plot some data growth_data.txt. Basically, it should plot a line graph showing a single line (or line + points) for the control and treated animals in this dataset. That is, one line for all the controls and one line for all the treated animals. Add appropriate error bars for each time point. But I don't know why the plot doesn't show the line and error bars on the plot which is weird.

What is wrong in my code? How to fix it? I included the plot I'm getting now.

...

ANSWER

Answered 2021-Oct-11 at 02:50

I'm sorry - I was incorrect about "Day" being a factor - thanks for fixing the broken link.

One potential solution is to add a 'group' aesthetic, e.g.

Source https://stackoverflow.com/questions/69519688

QUESTION

DESEQ2: varianceStabilizingTransformation Error: every gene contains at least one zero, cannot compute log geometric means

Asked 2021-Oct-08 at 05:55

I have a data-set comprising of an OTU table, where rows = samples and columns = OTUs, like this:

Otus <- data.frame(OTU_1 = c(0, 0, 1), OTU_2 = c(12, 0, 5), OTU_3 = c(0, 5, 3), row.names = c("S_1", "S_2", "S_3"))

I moved it from phyloseq over to DESeq2 using the phyloseq_to_deseq2 command without issue. Now that it's a DESeq2object, I want to normalize the OTU table using the variance stabilizing transformation with the following command:

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ANSWER

Answered 2021-Oct-08 at 05:55

What is your intended purpose for the variance-stabilized matrix? Are you then going to use the matrix to calculate differential abundance? In this tutorial, the authors (Susan Holmes and Joey McMurdie) refer to this tutorial for conducting differential abundance testing using the altered geometric mean formula, e.g.

Source https://stackoverflow.com/questions/69490402

QUESTION

Error in DESeqDataSet(se, design = design, ignoreRank) : counts matrix should be numeric, currently it has mode: logical

Asked 2021-Sep-27 at 16:33

I am running RNA Seq analysis on a dataset and I keep receiving this error when using DESeqDataSetFromMatrix. The df is counts data and the coldata is coldata.

Error in DESeqDataSet(se, design = design, ignoreRank) : counts matrix should be numeric, currently it has mode: logical Here is the code being used:

...

ANSWER

Answered 2021-Sep-27 at 16:33

I am not sure which version of R you use but a couple of things you can do is:

to indicate the separator (sep=",") when uploading your data frame with counts
you can also convert a data frame to numeric matrix using data.matrix()
go through DESeq2 vignette thoroughly. browseVignettes("DESeq2")

Source https://stackoverflow.com/questions/69349444

QUESTION

DESeq2 DDS filter error message using Dplyr

Asked 2021-Sep-24 at 19:38

dds$Description <- select(dds, Description == "Mammary_Tumor", "Mammary_Normal")
ddstxnmam <- DESeq2:: DESeqDataSetFromMatrix(countData = dds,
                                              colData = cd,
                                              design = condition)
ddstxnmam <- DESeq2:: DESeq(ddstxnmam)

...

ANSWER

Answered 2021-Sep-24 at 19:38

select is for selecting columns, you are filtering here ( at least it looks like that since you did not provide any description and did not add a dataset).

Source https://stackoverflow.com/questions/69261179

QUESTION

How to solve 'log2FoldChange is not numeric error' on R package EnhancedVolcano?

Asked 2021-Sep-02 at 10:29

I'm new to R and I'm trying to run R package EnhancedVolcano for generating a plot. My input csv file is a list of differentially expressed genes from DESeq2. The first column contains gene names that do not occur uniquely and so as to avoid duplicate rownames error, I decided to make.unique by adding .1 etc to the column 1 names as below. However, I keep getting the error log2FoldChange is not numeric!" for the below code

...

ANSWER

Answered 2021-Sep-02 at 10:29

Here is a potential solution:

Source https://stackoverflow.com/questions/69027615

QUESTION

Running DESeq2 from rpy2

Asked 2021-Aug-13 at 14:23

I am trying to run DESeq2 through rpy2 for the first time and am having some difficulties.

...

ANSWER

Answered 2021-Aug-13 at 14:23

If you open R and type:

Source https://stackoverflow.com/questions/68764734

QUESTION

magrittr pipe to righthand side in braces gives error

Asked 2021-Aug-03 at 21:54

I am using the magrittr pipe %>% to pipe an object into multiple arguments in the righthand side function, using curly braces to force :

...

ANSWER

Answered 2021-Aug-03 at 21:54

We can use

Source https://stackoverflow.com/questions/68643178

QUESTION

Cannot specify input dataset in shiny dashboard

Asked 2021-Aug-01 at 13:05

I am trying to make a shiny dashboard. I have two datasets, and based upon the selection of the datasets figures will be generate in the tab panels. However, by default only the last dataset that has been loaded/read is selected and I cannot select the first dataset. Even though I have made it default selection.

Below is my code.

...

ANSWER

Answered 2021-Aug-01 at 13:05

Assuming you have access to both datasets, you plot them both and display the selection. Try this

Source https://stackoverflow.com/questions/68606165

QUESTION

Snakemake with R script, error: snakemake object not found

Asked 2021-Jun-29 at 21:41

I'm having issues trying to run a snakemake rule that invokes an R script. The relevant snakemake rule looks like this:

...

ANSWER

Answered 2021-Jun-29 at 21:41

The examples use script: rather than shell: So change to

Source https://stackoverflow.com/questions/68185241

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

Vulnerabilities

No vulnerabilities reported

Install DESeq2

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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