Questions tagged [r]

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18
votes
4answers
8k views

How to compute RPKM in R?

I have the following data of fragment counts for each gene in 16 samples: ...
13
votes
4answers
3k views

What methods are available to find a cutoff value for non-expressed genes in RNA-seq?

I have a gene expression count matrix produced from bulk RNA-seq data. I'd like to find genes that were not expressed in a group of samples and were expressed in another group. The problem of course ...
5
votes
2answers
9k views

Manually define clusters in Seurat and determine marker genes

I want to define two clusters of cells in my dataset and find marker genes that are specific to one and the other. Is there a way to do this in Seurat? Say, if I ...
7
votes
3answers
3k views

Retrieve detailed gene descriptions

Given a list of gene IDs, how do you retrieve the gene description, summary and other detailed information in R?
0
votes
1answer
1k views

R studio failed to install the latest development version of hdf5r from Github (win10)

I install hdf5r following https://github.com/hhoeflin/hdf5r, it shows two methods: When I use the second method to install from github,it showed many errors: ...
8
votes
1answer
6k views

Extracting expression data from GSE dataset downloaded from GEO

I have downloaded GSE16146 dataset from GEO using GEOquery R package. I would like to extract "Data table" from downloaded GSE16146. ...
4
votes
2answers
3k views

How to convert a phylogeny to a dendrogram in R

I want to convert my phylogeny into a dendrogram so I can use it with dendextend in R to produce a tanglegram. I have made some progress but I keep encountering errors, see below: ...
2
votes
0answers
442 views

Filter out PCA outliers automatically

I am new to bioinformatics and PCA. What I am trying to do is to remove bad cells from a dataset that was obtained with scRNA-seq for ...
0
votes
0answers
122 views

about the scaling after normalization and transformation in RNA-seq data

When we use count data in RNA-seq analysis, we usually use normalization and sometimes vst, rlog transformation (DESeq2)or log2(CMP+4) transformation (edgeR) to perform K-means clustering. Can we use ...
-5
votes
1answer
72 views

Attempting to generate a heat map like in this figure [closed]

I have a data frame ...
18
votes
2answers
8k views

Understanding DESeq2 design, contrast and results

I have a set of high-troughput experiments with 2 genotypes ("WT" and "prg1") and 3 treatments ("RT", "HS30" and "HS30RT120"), and there are 2 ...
3
votes
1answer
5k views

Seurat with normalized count matrix?

I know that in Seurat we have the function CreateSeuratObject from which the analysis starts, but it accepts raw count matrix ...
5
votes
3answers
11k views

Resolution parameter in Seurat's FindClusters function for larger cell numbers

In Seurats' documentation for FindClusters() function it is written that for around 3000 ...
11
votes
3answers
6k views

Converting a VCF into a FASTA given a reference with Python, R

I am interested in converting a VCF file into a FASTA file given a reference sequence with Python or R. Samtools/BCFtools (Heng Li) provides a Perl script ...
8
votes
1answer
3k views

How to apply upperquartile normalization on RSEM expected counts?

I see that TCGA RNASeq V2 RSEM data is normalized with upper-quartile normalization. After doing Quantification with RSEM with the samples I have, I got "genes.results" as output which has gene id, ...
3
votes
4answers
500 views

Comparing phylogeny in R

So I want to compare the phylogeny created using two methods for example Maximum likelihood and maximum parsimony.Is there any way to compare the two phylogeny ? I did read about phangorn but not ...
5
votes
2answers
255 views

Assign cell types to groups of cells based on their gene expression profiles

I have large filtered, normalized dataset of scRNA-seq data of C.Elegans species. Rows are genes (10 000), columns are cells (66 ...
3
votes
3answers
587 views

Kruskal-Wallis rank sum test output confusion

I am running a multiple comparison using the non-parametric Kruskal Wallis test (K-W), using the ggpubr library and I am a bit confused about the results. When i just run the KW-test using "base R" ...
2
votes
1answer
2k views

3D PCA group labelling

I would like to make a 3D PCA but not sure how to label group wise which i can do for 2D PCA ...
1
vote
1answer
4k views

Changing active.ident in Seurat

Im trying to change the active.ident to another column in metadata but this error keeps popping up! I recently upgraded to R version 4.0.2 from 3.6.1 The older version was working but the new one isn'...
1
vote
2answers
340 views

Ranking metric in GSEA

I am using fgsea in r to calculate and plot a bunch of GSEA graphs. My question is whether it is acceptable to use the Wald statistic from DeSeq2 to rank the gene list? I have seen in the GSEA ...
0
votes
1answer
46 views

Best methods for clustering heatmap based on regions where the genes are most highly expressed?

I am analysing RNA-Seq data for a set of genes from different human brain regions using data from the Allen Brain Atlas. I have made a heatmap using GraphPad Prism. In this heatmap, I show the average ...
6
votes
3answers
500 views

Improve scRNA-seq dataset for further analysis

I got a dataset from C.Elegans scRNA-seq paper: GSM2599701_Gene.count.matrix.celegans.cell.Rdata in ...
5
votes
1answer
396 views

cell type specific genes - heatmap using rank based approach

I was wondering if some one can help me with pseudo r code for my approach here based on this paper to plot a heatmap Figure 3 Figure description The top 40 enriched genes percelltypeare shown in a ...
4
votes
2answers
195 views

Retrieving a list of human genes having GO associations

I need a command in R to retrieve all human genes associated with a Gene Ontology entry. I tried to look for it online but did not find it.
3
votes
1answer
312 views

Large dataset normalization for PCA

I need to normalize a large (400Mb) dataset for doing PCA analysis. I want to use scran for doing that: ...
2
votes
1answer
1k views

Pulling out a certain gene in a volcano plot

I have generated a volcano plot with a differential expression file. Code for inputing file: ...
2
votes
4answers
138 views

I have really skewed RNA-seq data, what's the best way to normalise it? Preferably in R!

My data frame compares the RNA-seq reads from many genes in different tissues. The reads look as follows. I tried using log to make it better but still looks pretty skewed. Are there any better ...
2
votes
1answer
79 views

Obtain CD (cluster of differentiation) marker expression information

There are 394 CD marker genes. Various resources (BD handbook, Abcam guide) contain information about which cell types express which CD markers. What is the best way to obtain or download this data so ...
1
vote
2answers
506 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 ...
1
vote
1answer
67 views

Merging files gives memory allocation error

I have two files like > head(a) chr position 1 1 136962 2 1 562020 3 1 672948 > class(a) [1] "data.frame" > And ...
1
vote
0answers
26 views

Data format for pathway based clustering of samples

I came across this paper as one of the examples from this paper, this one Figure 2. Host Protein Alterations in Infected iAT2s ...
0
votes
3answers
1k views

isSpike function in SingleCellExperiment package is deprecated?

I am trying to follow a tutorial from Sanger institute (from May 2019) on analysis of single cell RNA Seq data. They use isSpike function to filter out ERCC (control) and MT (mitochondrial RNA) reads, ...
0
votes
2answers
3k views

how to solve “dim(X) must have a positive length” at running ComBat function in R

I used ComBat() for batch effect correction in my expression data. basically, that function inputs are expression data, Batch covariate, and Model matrix for the ...
0
votes
1answer
52 views

Calculating Synonymous and non-synonymous

library(seqinr) library(ape) library(phangorn) alignment file data file sylvia.aln <- read.alignment("abhi_seq/all_seq_no_gal.fas", format="fasta") ...
0
votes
2answers
87 views

merge rows (to columns) in R dataframe based on IDs

I have a dataframe with two columns: $1 = transcript ID, $2 = expression counts (tpm). This comes from a merging of several ...
0
votes
1answer
95 views

alpha diversity wilcox.test

I am trying to do Wilcox test to detect the significant difference in alpha diversity but it is showing an error? physeqN2 is a phyloseq object and Season is a metadata column. ...
0
votes
2answers
131 views

parsimony and maximum likelihood tree comparison in R

Maximum Likelihood analysis compares the tips or the species based on their sequence similarity while Parsimony analysis compares the characteristic features among the species. So far I did ...
-4
votes
3answers
96 views

Selecting rows by partial match

I have a data frame one column is sample name like ...