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plink-ng

A comprehensive update to the PLINK association analysis toolset. Beta testing of the first new version (1.90), focused on speed and memory efficiency improvements, is finishing up. Future development will revolve around critical extensions to the core file format (multiallelic variants, dosage, phase).

ploidyngs

Explore ploidy levels from NGS data alone

plotly

Create interactive web graphics from R via plotly's JavaScript graphing library

plotly.py

An interactive, browser-based graphing library for Python :sparkles:

pmirdv

pophelper

An R package to analyse and visualise admixture proportions from STRUCTURE, fastSTRUCTURE, TESS, ADMIXTURE etc.

popnet

poppunk

PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)

popsizeabc

reformat of popsizeABC from Boitard 2016

powershell

PowerShell for every system!

ppspcp

A Plant Presence/absence Variants Scanner and Pan-genome Construction Pipeline

practical-guide-to-build-de-novo-transcriptome-assemblies-for-non-model-organisms

propagate

:exclamation: This is a read-only mirror of the CRAN R package repository. propagate — Propagation of Uncertainty

pseudohaploid

Create a pseudohaploid assembly from a partially resolved diploid assembly

psmc

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model

puppet-geneiouslm

Geneious Floating License Manager

pypgen

A population genetics module written in Python

python_biotrainee

Panda Shen's Python learning scripts

pythonngstools

Scripts for NGS processing

q2-feature-classifier

QIIME 2 plugin supporting taxonomic classification

qiime2

Official repository for the QIIME 2 framework.

qiimer

Quantitative Insights Into Microbial Ecology - parsing and plotting functions for R

quickmerge

A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.

quota-alignment

Guided synteny alignment between duplicated genomes (within specified quota constraint)

r-cmplot

📊 Circular Manhattan Plot

r-color-palettes

Comprehensive list of color palettes available in r ❤️🧡💛💚💙💜

racon

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116

rad_tools

A collection of usefull tools for RAD or GBS data analysis

ragoo

Fast Reference-Guided Scaffolding of Genome Assembly Contigs

raisd

RAiSD: software to detect positive selection based on multiple signatures of a selective sweep and SNP vectors