Questions tagged [r]

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Issue doing differential gene expression with an ordinal variable

I'm trying to figure out the right way to do differential gene expression analysis with a discrete variable. The context is, I want to assess differential expression as a function of whether samples ...
1 vote
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analysing node connectivity difference in a continuous scale (edge weighted by correlations)

I have an edge list object weighted by a correlation value. I would like to know the changes in the node's connectivity on a continuous scale. In other words, how does the node connectivity differ ...
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Batch correction in differential expression analysis

I have sent two sets (two batches in matter of sending for sequencing) of different samples (plasma) to small RNA-seq to Qiagen company This is how my meta data look ...
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1 answer
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How to highlight the specific peptide sequences after performing multiple sequence alignment for the fasta file?

I have the peptide sequences and fasta files separately. I first aligned the fasta files using msa package. After that I'm trying to highlight the peptide sequences ...
3 votes
2 answers
125 views

dealing with a list of VEP files

I'm new to dealing with big and compressed data so, I have some questions regarding that I have 1000 files, each file has the extension (vep.txt.gz) I want to read these files, then filter them. The ...
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1 answer
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Retrieve rsIDs from chromosome positions using MRutils::get_rsid_from_position

I have 5609 chromosome positions with both ref and alt alleles. I want to retrieve rsIDs for the same. I tried get_rsid_from_position() of the ...
1 vote
2 answers
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How to apply a mathematical function to a matrix in R

I have a matrix that looks something like this: chr pos het chrI 27 2 chrI 55 0 chrI 27 0 chrI 55 1 It's essentially a VCF file that I have converted into a TSV. I want to be able to take all ...
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2 votes
1 answer
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Should be RT-qPCR values standardized before PCA analysis?

I come from this question of gene exression analysis: Should PCA be standardized for gene expression? My experiment is based in 151 x 51 (individuals/samples x genes), in which, patients are subjected ...
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2 answers
127 views

Merge data frame on either of the 2 columns in R or python

I have two data frames. One data frame with one column and second data frame with two columns. I need to merge first data frame with either column of the second data frame and returns the values. ...
2 votes
0 answers
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Using R `ggtree`, attach extra data next to the nodes on an illustrated tree/newick file

This is really a programming question but ggtree might be too obscure for this question to be posted on StackOverFlow as a general R related question. I am having ...
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Why It is not possible to open the file when I use open_loom() function in R?

I'm using the SCENIC package in R to analyze single-cell RNA-seq data. This is the script based on the main tutorial. ...
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Expending UpsetR plot with Orthofinder families and gene numbers

I can create an Upset plot with the input file, which can be found here ...
3 votes
2 answers
130 views

DESeq2 for large number of samples takes too much RAM

I am trying to run a very large number of transposase-accessible chromatin (ATAC)-seq samples through DESeq2 to find peaks of differential chromatin accessible across my study genome. I have about 100 ...
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1 answer
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Manually order the set fails in UpsetR

This question was also asked on Biostars I have tried to use UpsetR to visualise the input file, which can be found here. How is it possible to make UpsetR accept an order defined in ...
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1 answer
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Identify SNP from genetic position

I am looking for a way to obtain SNP names from their coordinates (Chromosome:BP) - very much the reverse of the question answered here: (https://stackoverflow.com/questions/20251612/map-snp-ids-to-...
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2 votes
1 answer
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Can I run dotPlotly from Rstudio?

I'd like to run dotPlotly from RStudio but I can't find any description/help for this. Is it at all possible? Another side to this question: does anyone know any tool for dot plots for genome ...
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3 votes
1 answer
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How to make bar bigger in UpsetR plot

I have tried to use UpsetR to visualize the input file which can be found here. ...
2 votes
1 answer
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Coexpression network analysis

I have a question related with the most popular frameworks for network construction: WGCNA for weighted networks and igraph package for unweighted networks. What are the advantages or disadvantages of ...
2 votes
1 answer
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What are the conditions to perform Gene Expression Analysis on data you've performed RNA Sequence Analysis on?

I want to perform Differential Gene Expression Analysis. I recently completed RNA Sequence Analysis using the Seraut Tutorial up to this point: Finding Differentially Expressed Features (Cluster ...
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Could someone help me understand if all sample within this are control group?

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117872 I'm teaching myself sequence analysis. This is the count data: and then this is, what I believe to be, the coldata: All I want to know is ...
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1 answer
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Keep first 20 nucleotides of sequences using R

I have an Excel sheet from the CRISPR library where I have sequences of gRNAs (with 30 nucleotides) in a column and I only need to keep the first 20 nucleotides for those gRNAs and delete the rest ...
1 vote
1 answer
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Can I perform Expression Analysis on this 10x dataset?

10x Genomics: 20k Human PBMCs is the dataset. Description of the dataset: Inputs/Libraries Human peripheral blood mononuclear cells (PBMCs) of a healthy male donor aged 30-35 were obtained by 10x ...
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1 answer
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file path of BiocManager:install()

I was trying to format my GWAS summary statistics with the MungeSumstats R package and would need to install ...
0 votes
1 answer
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replacement has 1 row, data has 0

I have tried to use UpsetR to visualize the input file which can be found here ...
2 votes
0 answers
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LD block labels annotation for GWAS summary data

I have a txt file summarising the result of a GWAS on an European population. Its structure is the next one: ...
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1 vote
1 answer
281 views

How to resolve Error in fix.by(by.x, x) : 'by' must specify a uniquely valid column while using merge function in R

I have two csv formatted data frames that I want to merge. First data frame contains 9 columns and the second contains three columns. Based on column names: start, end, function I am trying to merge ...
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2 votes
1 answer
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Turning GMT file into data frame so that third column is comma seperated

Similar to: How to convert data in gmt format to dataframe? I have downloaded a GMT file from the GSEA database (https://www.gsea-msigdb.org/gsea/msigdb/download_file.jsp?filePath=/msigdb/release/2022....
1 vote
1 answer
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Why do I have missing values returned from getBM when converting Ensembl transcript IDs to gene names?

When I run the following R code to convert Ensembl transcript IDs to gene names and Ensembl gene IDs: ...
0 votes
2 answers
53 views

How to find restriction enzyme frequency in whole genome and count the distance between them?

I am having possibly a simple question which is proving difficult. My objective is to take the reference FASTA file and flat file database with 1500 restriction enzymes with its cutting sites (mostly ...
1 vote
2 answers
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How to identify matching and unique rows across different columns in R data-frame?

I am working on a large data-frame that has 4 columns and each column has variable rows. I am trying to find unique and identical pathways between the 4 columns (each column represents a particular ...
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0 answers
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hypergeometric test in R

I have 15800 genes in a dataset, of which 5233 are differentially expressed, of which 1707 are upregulated. I have a second population of 17763 genes, I have selected a group of 119, of which 65 are ...
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1 answer
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How to find closely related genes for a specific gene from WGCNA modules?

I have used WGCNA by integrating several datasets which are processed in a similar way. Identified 17 modules, followed by performed pathway analysis with the genes present in those modules. Among all ...
3 votes
1 answer
73 views

heatmap of specific sequence motifs in aligned fasta files

I have a collection of fasta files, each containing three aligned sequences. I am interested in understanding the distribution of a specific sequence motif PGP, RGP and KGP in all the alignments. I ...
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1 vote
2 answers
77 views

Error in dimnamesGets(x, value) when trying to read data using Seurat package

This question has also been asked on Biostars I am trying to create a Seurat object using the package "Seurat". When I am reading my raw files using the function ...
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5 votes
3 answers
72 views

Ubiquitous regulation of highly specific marker genes

I am fairly new to scRNAseq analysis and keep running into the same problem in the two datasets I am currently working with. We work with kidney inflammation and have two new mouse models, which we ...
0 votes
1 answer
51 views

subset from a dataframe using other dataframe in R

I have a data frame (named as df) with single column of protein IDs and other file with two columns of protein IDs (named as df1). I need to find the df IDs present in either first or second column of ...
1 vote
0 answers
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Clustering individuals by gene presence/absence

I have a binary matrix with individuals as row names, and gene name as column name. So, if the gene is present in an individual, we have 1, otherwise 0. I would like to cluster individuals based on ...
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2 answers
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Is it possible to integrate multiple gene expression datasets and use it for WGCNA?

I have 8 RNA-seq datasets and am interested in looking at genes co-expressed with a specific gene. Among 8 RNA-seq datasets, 6 have less than 20 samples. Rather than working on each dataset ...
2 votes
1 answer
34 views

How to plot stacked bar chart using R showing mean with range and labelled values?

I am trying to plot a stacked bar graph with mean values from multiple repeats, also showing the range of the data and values labelled. My data frame is below: ...
1 vote
1 answer
50 views

How to get started with louvain/leiden algorithm with UMAP in R

A collegue of mine recently suggested to try the louvain algorithm for clustering multiplex cytometry data. However, implementations of louvain are kind of rare in R. To my knowledge the only stand-...
0 votes
0 answers
20 views

MLPE in lmer (lme4 in R)

I am trying to conduct some landscape genetics analysis by testing association between landscape resistance matrices and pairwise genetic distances using linear mixed models. When I run lmer package, ...
0 votes
1 answer
64 views

select highly variable genes out of dataframe

lets say I have the following dataframe: ...
1 vote
0 answers
34 views

Cannot run `loadData()` after saving RDS file and reading RDS file using `saveRDS` & `readRDS` in Seurat

I want to load multiple sample data(pbmc16 and pbmc45), and integrate by following the tutorial below Performing integration on datasets normalized with SCTransform https://satijalab.org/seurat/...
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2 votes
0 answers
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I am trying to use slingshot for pseudotime analysis. I am getting error while saving an object as dataframe

When I run following code, I get error at - slingshot_df <- data.frame(colData(sce)) the error is : Error in as.vector(x) : no method for coercing this S4 ...
0 votes
1 answer
56 views

Merge/Join one data frame (X) to multiple data frames separately

Let us say that we have some data frames named S1,S2,S3... that I want to join independently by column names to dataframe X. This is how they look like: ...
1 vote
1 answer
27 views

Creating multiple phenotype datasets using bootstrap method "Bootstrap-samples-by-column-of-a-data-frame-in-r" for DEG analysis

I am working on a datasets and after some discussion with my group, we doubt that maybe one or more of our controls are different than the other controls. The motivation is to see if one or more ...
1 vote
0 answers
33 views

How to tune and use the MetaVolcanoR package

I conducted a differential expression analysis over several datasets, using LIMMA, each one on its own. For each dataset, I have a data frame of all the genes, with ...
3 votes
2 answers
75 views

How should I interpret DGE results if only one HLA-A gene shows up as significant but not the others?

I have done a DGE recently and have been looking at the DGE list. One of the genes is HLA-A. However, when I dug deeper I realised there are hundreds of HLA-A genes with unique ENSEMBL number (of ...
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1 vote
0 answers
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difficult in runing the R code for ggtree

I tried to run the below code but ended having issue. I have checked thoroughly and I didn't find any mismatch in fasta sequence ...
1 vote
1 answer
122 views

Error of duplicated rownames although there are no duplicates

I have a data frame that I want to switch its row names from EnsembleID (GENEID) to gene symbol (SYMBOL). When I try to switch, I get this error: ...

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