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Questions tagged [r]

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0
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1answer
17 views

How I deal with this expression set?

I have a gene expression raw counts like below for 16 patients ...
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1answer
22 views

Tree cut issue in WGCNA

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0
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1answer
38 views

correlation between transposon and gene

I have two matrix identical in N° of rows and columns. In the first matrix rows indicate transposable elements and columns indicate samples. the matrix show the degree of expression of each element ...
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2answers
35 views

Which correlation method to compute the correlation score between different clusters of Sc-RNAseq data?

I'm analyzing single cell rna-seq data and trying to compute the correlation score between different clusters. Wondering how to choose the correlation method("pearson" (default), "kendall", or "...
1
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1answer
87 views

Doing plot with this data

I have normalized expression values of some genes in some patients and the how many days they have survived from their diagnosis with cancer like below EDITED I have taken mean of the expression ...
2
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2answers
56 views

How I swap rownames in these data?

I have a microarray gene expression matrix like this by weird gene IDs in rows. > head(mat[1:10,1:5]) > dim(mat) [1] 39302 76 > There is matched ...
1
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2answers
28 views

How to retrieve values from one table that corresponds to the values in another table in R

I have following table. structure(list(n = c(29L, 11L, 10L, 10L), domain = c(1L, 5L, 6L, 32L)), row.names = c(NA, -4L), class = c("tbl_df", "tbl", "data.frame")) ...
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2answers
23 views

R WGCNA error code

I am using WGCNA to identify Consensus modules. I get a warning message when completing the following step: Call the network topology analysis function for each set in turn Warning: ...
0
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1answer
46 views

Investigate the effect of street-light regime on insects

I need advice on a suitable analysis of a dataset that has an awkward design - because we investigate a real-world situation -we have two sites (A,B) where we can conduct the research. The hypothesis ...
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0answers
31 views

Row labelling in a heatmap in R

Could I have specific row labels in bold text but not all of them when creating a heatmap using R? (eg. using heatmap.2 function)
1
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1answer
17 views

How to map selected genes to Metabolic pathway Maps

I have a selected Arabidopsis Genome Initiative (AGI) list for RNA seq and proteomics data, how can I map them to metabolic pathway maps to vilualize(e.g. TCA cycle / FA / Photosynthesis) in KEGG or ...
2
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1answer
38 views

How to load and split my two individual datasets when integrating datasets in Seurat?

I want to do comparative analyses of my two individual single cell RNA-Seq datasets in Seurat. And I load and list my data as follows: ...
0
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0answers
34 views

Create a Heatmap that uses modules of genes rather than individual genes in Seurat

Is it possible to create a Heatmap in Seurat that takes in and displays modules of genes as its features rather than individual genes? So if I have a module of genes associated with a trait or ...
0
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0answers
21 views

module differential connectivity (MDC) analysis

Paper in this paper I am citing the lines below . ) Intra-modular connectivity of resilient and susceptible network modules was compared to that of corresponding genes in control mice to identify ...
0
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1answer
60 views

Changing the axis limits of ggplot objects

By EnhancedVolcano R package I have this plot with this code ...
0
votes
1answer
78 views

How I deal with this kind of gene expression comparision

I have RNA-seq from two sequencing batches; Lab technician says that he has run the RNA expression quantification two times in bathes 1 and 2 for example tumor 1 in batch 1 and tumor 1 in batch 2 , ...
0
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0answers
27 views

Module preservation analysis WGCNA

I have done a WGCNA (weighted gene co-expression network analysis) analysis for various brain disorders. So along with control, I have 3 different disorders such as BPD, MDD and SCZ. Now I have to ...
0
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2answers
76 views

Interpreting this PCA plot for RNA-seq

I have RNA-seq from two sequencing batches; Lab technician says that he has run the RNA expression quantification two times in bathes 1 and 2 for example ...
0
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0answers
39 views

Want to make a tsne plot show subset

I am new to R. I make a tsne plot for my data "yfp". And there are two subsets in my data (yfppt and yfpng). I want to show their distribution or location in yfp tsne plot but failed. And I even did ...
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0answers
33 views

How to run function “convolve” in parallel in R?

I have a vector of 200 million numbers. It has been running for over 24 hours and still not done. ...
0
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1answer
23 views

Biplot scores from canonical correspondence analysis

I'm using the R package vegan to perform canonical correspondence analysis (CCA). As input we have two matrices, one being (sites)x(species) and the other being (sites)x(conditions). Sample data (...
2
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1answer
52 views

Create a Grouped Barchart

I’m trying to create a Group Chart like this: I have 7 classes for each of 4 species, not 5 like in the diagram. I want to build i diagram to show the distributions of the classes in each species ...
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0answers
27 views

how to cluster data separately based on HTO tags

If I have 2 samples hashed, ran together and generated one ADT file for them, then how do I plot 2 different ADT clusters separated based on the hashtags. I did use HTOdemux, but it shows me ...
1
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1answer
39 views

How do I create a filtered gene list using expression medians

Forgive the simple noob question I have TPM data of ~50k genes (rows) across ~1k cell lines (columns). In R, I would like to output an "intermediate expression" gene list for each cell line, like: <...
1
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0answers
54 views

Argument stopped working

I am using ComplexHeatmap package for transcriptomic analyses and all of a sudden, row_labels and column_labels as well as <...
0
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1answer
30 views

Mapping probe ID to gene name

I have set of modules from various condition ,with first column as Probe_ID name and I have an annotation file with Probe_ID and Gene_name. I have to map the Probe_ID to gene name in each file and ...
1
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0answers
42 views

Identification of differential genes across 8 groups [closed]

I need to identify differential genes across 8 groups. I know this can be done using DESeq2 or EdgeR as these are better suited and equipped. However, I was thinking if something like this piece of ...
0
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1answer
61 views

Creating a count table using R

I’m trying to develop a table from a series of lists generated using the Immunarch library to process TCR sequencing results. Each list is comprised of CDR3.aa (clone) information which are character ...
1
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0answers
38 views

Error using bseqsc

I will be very grateful for any hint on how to overcome the error. I wish to deconvolve my bulk RNA seq data obtained from the lungs of mice using single cell RNA seq data. For practice, I am ...
0
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1answer
74 views

How to transform and sort the matrix to make a heatmap showing signatures?

I have a matrix data with cells as rows and samples as columns. Here I am giving the data with dput ...
0
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0answers
31 views

How can extract the list of genes name from the raw data in GEO?

The format of the raw data that upload in GEO is different, like TXT, CEL or other form. How can I extract the list of genes name from these formats? And then how can I normalize them with R? I would ...
2
votes
1answer
101 views

Multiple line chart

I am trying to create a multiple coloured line graph based on six lines. Essentially I have data that identifies different units of vegetation by the variable” NDVI (vegetation index)” I want to ...
0
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1answer
99 views

Intersecting multiple data frames

I have to intersect multiple data frame to find common elements. For visualization purpose i can use upset Plot but it doesn;t return a object containing the intersection object .I tried jvenn but at ...
0
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2answers
42 views

How to retrieve the subcellular location info from uniprot?

I have a list of proteins with their gene names/symbols. I would like to identify which of them are extracellular proteins or plasma membrane proteins. I can get this information in UniprotKB by ...
0
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0answers
8 views

Cannot use .owl files downloaded in PANTHER with paxtoolsr functions

I am trying to transform a PANTHER pathway into a GSEA-appropriate format. For this, I am trying to execute the following code taken from paxtoolsr documentation ...
1
vote
1answer
111 views

Ternary plot in R

I have plotted a triangular plot,that three dimensions of which represent three herbal strategies. One dimension represents the strategy of C (competitive plant), the second dimension “S” (stress ...
1
vote
1answer
53 views

How do I select a proper design matrix to use in DRIMSeq?

I am trying to use DRIMseq for DTU with 2 treatments on two different strains of an animal model. How do I select a proper design matrix to use in DRIMSeq ? How I know that one is the correct one to ...
0
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0answers
18 views

Mapping GPL Platform Number to Microarray Name

I am trying to download a dataset from GEO using the GEOquery R package. Using this package, I can retrieve the GPL platform number(s) for the dataset, and I hope to use a CDF file from BrainArray on ...
1
vote
1answer
79 views

Hierarchical clustering for outlier detection - single cell RNASeq & WGCNA

I wish to conduct WGCNA on a single cell RNASeq dataset and, when choosing the optimal beta parameter after running pickSoftThreshold am presented with a rather ...
1
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0answers
75 views

Normalization of single cell RNASeq data with ERCC spike-ins

I wish to normalize a scRNASeq dataset with respect to ERCC spike-ins, where "for some of the samples, ERCC spike-in RNA was added to the lysis buffer" and was wondering how to do so? I have seen ...
3
votes
1answer
85 views

Subsetting of object existing of two samples

I have a Seurat object existing of an aggregate of two samples namely; RD1 and RD2. I am trying to make a subset of each sample. But it's not really working. I manage to make a subset of the cells but ...
1
vote
1answer
38 views

rentrez to retrieve NIH files

I'm trying to use rentrez package to retrieve NIH files, and ran the following code (I followed what was on the rentrez tutorial): ...
1
vote
1answer
305 views

DoHeatmap Hierarchical Clustering Seurat

I have a list of genes that I'd like to visualize using the DoHeatmap function in Seurat. However, the output of the heatmap does not result in hierarchical clustering and therefore makes it very ...
2
votes
1answer
111 views

Using `install.packages` with conda-managed R

I have R installed and managed by conda (miniconda) on my MacBook Pro. The version of R I use most frequently (3.5.1) is installed on the base environment and I have other version-specific ...
-1
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1answer
41 views

R error: could not find function “pathwayAnalysis”

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0
votes
1answer
73 views

Why is 42 the seed used in RunPCA() in Seurat?

The RunPCA() in Seurat 3.0 function has seed.use=42 by default. How does one choose a seed number? Is this chosen simply because ...
0
votes
1answer
42 views

Error: package or namespace load failed for 'ChIPseeker'

How do I solve the problem of loading the bioconductor Chipseeker package? I have installed in the following way and I having an error while loading it and I do not know why. ...
1
vote
0answers
40 views

How can I correctly get 3D scatter plot for micro-array pheno data in R [updated]?

I intend to see data points distribution (each reows) within labeled groups (different batchs such as 1,2,3, and so on) in 3D scatter plot, because I want to see the distribution of the data points ...
0
votes
1answer
42 views

Reducing a string to a certain amount of the first characters in R

So I have a list of several thousand RNA transcripts, and I am trying to find out how they are spliced. Right now I am running matchLRpatterns() from the Biostrings ...
0
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0answers
30 views

Create samples of cells for the limma package

I have an aggregated sample that consist of yellow and non-yellow labeled cells. The objective is to find differentially expressed genes between these two groups of cells using the limma package. How ...