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Questions tagged [r]

Please supplement your question with a minimal reproducible example. Use dput() for data and specify all non-base packages with library calls. For statistical questions please use http://stats.stackexchange.com.

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Calculating total number of Unique gene in every genome from ROARY pangenome output

I performed a ROARY from 100 genome. I got several file including gene_presence_absence.csv from the results. I want to know how many unique gene(unshared gene, based on blast homology, same gene (...
Umar's user avatar
  • 135
1 vote
1 answer
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To find genes that don't change in RNA-seq, Deseq2 has altHypothesis="lessAbs". Is there a way to make limma do the same thing for proteomics?

I love that Deseq2 has altHypothesis="lessAbs" !!!!!!! I've used it a ton for RNA-seq. However, now I'm working with mass spect data using limma. Is there a way to make limma do the same ...
Mary Allen's user avatar
1 vote
0 answers
46 views

What is the best approach to do a PCA analysis to distinguish between two groups?

I have two samples A and B and I do have an RNAseq for both of them. Inside each file (for A and B) I do have a set of FPKMs that give me a fold change for each gene (sample vs control). It looks ...
Lara's user avatar
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3 votes
1 answer
266 views

Plot phylogenetic tree from list of edges

I have a dataset that I wish to convert to tree or phylo format like in the ape package, in order to plot the phylogenetic tree. It is formatted like a list of ...
helle's user avatar
  • 33
1 vote
0 answers
43 views

Naming functions in R

I have a set of files based on which I expect to load RDS files like R1-Tn5-NHP-55_NA and R1-Tn5-NHP-42_NA but the code is producing just the name of the 55 files not both 55 and 42. ...
Aranyak Goswami's user avatar
2 votes
0 answers
90 views

Filter phyloseq sequence table

I have phyloseq object where sequence table were builded by using the function mergeSequenceTables from DADA2 package, to merge ten sequence tables from different runs. The sample_data consist of two ...
77__bio's user avatar
  • 21
3 votes
1 answer
93 views

Sanger Sequencing Knitting Error

I am doing a project where I am reproducing the analysis from the article "sangeranalyseR: Simple and Interactive Processing of Sanger Sequencing Data in R". Below is the example chunk for ...
Taeen Jidaan's user avatar
-1 votes
2 answers
60 views

To find amino acid substitution from fasta alignment

I have fasta multiple sequence alignment file of protein sequence. I want to look for mutation/substitution in amino acid between query with reference to one query. Is there any R package or any ...
Shweta Kumari's user avatar
1 vote
0 answers
29 views

Normalization and Merging of Gene Expression Panels with Overlapping Genes from Same Cohort

I have done some gene expression work using two Nanostring panels (glial profiling and neuroinflammation) on the same 18 tissue samples. There are some overlapping genes between the panels, about 150 ...
Carolyn's user avatar
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1 vote
1 answer
75 views

GLM for multinomial using r - results of genotyping

I have next data: age - how old is person, e.g. 17 or 25 bmi - body mass index, e.g. 18.25 or 29.35 rsXXX - results of genotyping in rs(point), e.g. rs10852521: C/C, C/T and T/T I devide all data ...
n.osennij's user avatar
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2 votes
0 answers
47 views

Using Multi-Dimensional Scaling (MDS) to produce a vector in order to account for patient bias when constructing DGE lists from RNA-seq datasets in R?

I am currently working on my PhD and as part of my thesis, I intend to analyse gene expression within multiple sclerosis (MS) lesions by looking at RNA-seq datasets on Gene Expression Omnibus (https://...
R_Cres_01's user avatar
1 vote
1 answer
117 views

Phylogeny building in R from FASTA files:

Im working on building a phylogeny from scratch with downloaded FASTA sequences from GeneBank. I think Im doing alright up until the multi sequence alignment in the ...
I Del Toro's user avatar
2 votes
1 answer
153 views

Is there a way to calculate the number of parsimony informative characters in a morphological dataset in R?

I have a dataset of binary morphological characters and would like to know how many of them are parsimony informative. Is there a way to calculate this with an R package?
Namenlos's user avatar
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4 votes
2 answers
65 views

question to pick values based on conditions using a loop

I have a dataset with following information. Column C1_1 is chromosome number, C1_2 is SNP position and C3 is the p-value. I want to pick the most significant association within a genomic region of ...
user1567654's user avatar
3 votes
2 answers
891 views

How do I change the legend for a Violin Plot with median dot

I'm plotting scRNA data using Violin Plots. I need to re-order the plots and add median dots. My code is: ...
WantaghMomma's user avatar
1 vote
1 answer
617 views

Differential gene expression: how do I correctly compare three groups to each other?

I'm trying to figure out the right way to do differential gene expression analysis with a discrete variable with three groups. The context is, I want to assess differential expression as a function of ...
mrz123456's user avatar
1 vote
0 answers
16 views

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 ...
data's user avatar
  • 123
0 votes
1 answer
120 views

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 ...
Zizogolu's user avatar
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0 votes
1 answer
107 views

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 ...
Lazy PhD's user avatar
3 votes
2 answers
302 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 ...
Joman's user avatar
  • 39
1 vote
1 answer
809 views

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 ...
Jyoti Sharma 's user avatar
1 vote
2 answers
124 views

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 ...
rimo's user avatar
  • 1,003
3 votes
1 answer
140 views

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 ...
Javier Hernando's user avatar
-2 votes
2 answers
432 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. ...
user avatar
2 votes
1 answer
396 views

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 ...
Sudoh's user avatar
  • 217
3 votes
0 answers
520 views

Expending UpsetR plot with Orthofinder families and gene numbers

I can create an Upset plot with the input file, which can be found here ...
user3523406's user avatar
3 votes
2 answers
554 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 ...
Shashank Nagaraja's user avatar
0 votes
1 answer
218 views

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 ...
user3523406's user avatar
0 votes
1 answer
613 views

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-...
Gux's user avatar
  • 103
2 votes
1 answer
117 views

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 ...
SKay's user avatar
  • 23
3 votes
1 answer
246 views

How to make bar bigger in UpsetR plot

I have tried to use UpsetR to visualize the input file which can be found here. ...
user3523406's user avatar
2 votes
1 answer
119 views

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 ...
María José's user avatar
2 votes
1 answer
62 views

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 ...
Antonio's user avatar
  • 129
1 vote
0 answers
34 views

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 ...
Antonio's user avatar
  • 129
0 votes
1 answer
42 views

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 ...
user16558's user avatar
-1 votes
1 answer
88 views

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 ...
Antonio's user avatar
  • 129
1 vote
1 answer
247 views

file path of BiocManager:install()

I was trying to format my GWAS summary statistics with the MungeSumstats R package and would need to install ...
Lloyd_LiuSiyi's user avatar
0 votes
1 answer
486 views

replacement has 1 row, data has 0

I have tried to use UpsetR to visualize the input file which can be found here ...
user3523406's user avatar
2 votes
0 answers
56 views

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: ...
Gero's user avatar
  • 73
2 votes
1 answer
4k 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 ...
kumuda's user avatar
  • 23
2 votes
1 answer
97 views

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....
tacrolimus's user avatar
1 vote
1 answer
299 views

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: ...
An Ignorant Wanderer's user avatar
0 votes
2 answers
197 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 ...
Santosh's user avatar
1 vote
2 answers
514 views

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 ...
salman1490's user avatar
0 votes
1 answer
145 views

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 ...
user9114's user avatar
3 votes
1 answer
196 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 ...
Jalan's user avatar
  • 31
1 vote
2 answers
361 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 ...
Gen's user avatar
  • 21
5 votes
3 answers
127 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 ...
Smeerlap's user avatar
0 votes
1 answer
227 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 ...
user avatar
1 vote
0 answers
155 views

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 ...
Marco's user avatar
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