Category "bioinformatics"

app$vspace error in building phylogenetic tree in R

I am working with phylogenetic trees. Import the phylogenetic tree file with ggtree::read.tree and get the information with readxl::read_xlsx. I want to visuali

Abnormal termination of R session on Rstudio server with DECIPHER alignment

I am running an alignment with the DECIPHER package in bioconductor using an Rstudio instance located on a server. dna1 <- RemoveGaps(dnaSet, removeGaps = "a

Is there a faster way to find synonyms for a large list of taxa in R?

I have a list of about ~96,000 species names I need to collect all synonyms for. I have tried the 'taxize' package with the synonyms() function, which outputs t

Number of items to replace is not a multiple of replacement length when using a for loop

First, I parsed the AAChange.refGene column from the variant_calls dataframe and then extract the Refseq ID, cDNA level change, and Protein level change informa

Bowtie2 error : " does not exist or is not a Bowtie 2 index"

I'm very new to bioinformatics and RNA-seq so go easy on me. I keep getting the same error when I try perform my analysis. For background: I have a folder calle

ungapped index for biopython alignments

My first time using biopython. Forgive me if this is a basic question. I would like to input sequences, then align them, and be able to refer to the index posi

How to handle multiple optimal edit paths implementing Needleman-Wunsche algorithm?

Trying to implement Needleman-Wunsche algorithm for biological sequences comparison. In some circumstances there exist multiple optimal edit paths. What is th