Top 4 R Bioinformatic Projects
command line bioinformatic scripts written in RProject mention: Splitting multifast file into individual single fasta R | reddit.com/r/bioinformatics | 2021-08-09
https://github.com/olgatsiouri1996/biomisc_R/blob/main/fasta_manipulation/split_multifasta_to_singlefasta.R this will help. I would recommend using sed to keep only the ids and not the full fasta headers
Simple R utilities for working with HMMERProject mention: how to work with a hmmsearch table output? | reddit.com/r/bioinformatics | 2021-07-18
I use this R package in Rstudio; https://github.com/arendsee/rhmmer
Scout APM: A developer's best friend. Try free for 14-days. Scout APM uses tracing logic that ties bottlenecks to source code so you know the exact line of code causing performance issues and can get back to building a great product faster.
R wrapper for ermineJProject mention: Gene ontology of differentially expressed genes in R | reddit.com/r/bioinformatics | 2021-08-04
I would recommend ermineJ as thier statistical approach is better suited to overcome issues with how GO is constructed and the imbalance in the sizes of GO terms (sizes meaning the number of genes assigned). They have a graphical, command line interface and an R package link
Baltica: integrated differential junction usage (DJU)Project mention: Novel Splice Variants in RNAseq Data | reddit.com/r/bioinformatics | 2021-09-15
Also, we've been working on a framework with multiple workflows for differential splicing: Baltica: integrated differential junction usage (DJU) https://github.com/dieterich-lab/Baltica . Please have on mind that Baltica is work in progress, but the workflows are quite mature. Fell free to contact me if you have any questions!
What are some of the best open-source Bioinformatic projects in R? This list will help you:
Are you hiring? Post a new remote job listing for free.