R Bioinformatics

Open-source R projects categorized as Bioinformatics | Edit details

Top 4 R Bioinformatic Projects

  • GitHub repo biomisc_R

    command line bioinformatic scripts written in R

    Project 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

  • GitHub repo rhmmer

    Simple R utilities for working with HMMER

    Project 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

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    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.

  • GitHub repo ermineR

    R wrapper for ermineJ

    Project 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

  • GitHub repo Baltica

    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!

NOTE: The open source projects on this list are ordered by number of github stars. The number of mentions indicates repo mentiontions in the last 12 Months or since we started tracking (Dec 2020). The latest post mention was on 2021-09-15.

Index

What are some of the best open-source Bioinformatic projects in R? This list will help you:

Project Stars
1 biomisc_R 20
2 rhmmer 10
3 ermineR 4
4 Baltica 2
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