davised

lapce

Lightning-fast and Powerful Code Editor written in Rust

vim-surround

surround.vim: Delete/change/add parentheses/quotes/XML-tags/much more with ease

miller

Miller is like awk, sed, cut, join, and sort for name-indexed data such as CSV, TSV, and tabular JSON

ultisnips

UltiSnips - The ultimate snippet solution for Vim. Send pull requests to SirVer/ultisnips!

fantasque-sans

A font family with a great monospaced variant for programmers.

rich-cli

Rich-cli is a command line toolbox for fancy output in the terminal

plasticity

bitburner

Bitburner Game

contour

Modern C++ Terminal Emulator

moe

A command line based editor inspired by Vim. Written in Nim.

rstatix

Pipe-friendly Framework for Basic Statistical Tests in R

taxonkit

A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV

ggside

ggplot2 extension allowing for plotting various geometries as side panels using the ggplot2 API

arriba

Fast and accurate gene fusion detection from RNA-Seq data

explore

R package that makes basic data exploration radically simple (interactive data exploration, reproducible data science)

faqtory

A tool to generate FAQ.md documents and automatically suggest answers to issues

CAMISIM

CAMISIM: Simulating metagenomes and microbial communities

BioSequences.jl

Biological sequences for the julia language

run_dbcan

Run_dbcan V4, using genomes/metagenomes/proteomes of any assembled organisms (prokaryotes, fungi, plants, animals, viruses) to search for CAZymes.

platon

Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.

microViz

R package for microbiome data visualization and statistics. Uses phyloseq, vegan and the tidyverse. Docker image available.

PIRATE

A toolbox for pangenome analysis and threshold evaluation.

geta

pseudofinder

Detection of pseudogene candidates in bacterial and archaeal genomes.

BASTA

Basic Sequence Taxonomy Annotator

mitohelper

Mitohelper: a mitochondrial reference sequence analysis tool for fish eDNA studies

mitoVGP

The Vertebrate Genomes Project Mitogenome Assembly Pipeline

fastax

Make phylogenetic trees and lineages from the NCBI Taxonomy database

superspreadingdispersion

NAAMES_2020

NAAMES Amplicon analysis (stations of the four cruises)