mt1022

rustlings

:crab: Small exercises to get you used to reading and writing Rust code!

pytorch_geometric

Graph Neural Network Library for PyTorch

GNNPapers

Must-read papers on graph neural networks (GNN)

scientific-visualization-book

An open access book on scientific visualization using python and matplotlib

janitor

simple tools for data cleaning in R

cutadapt

Cutadapt removes adapter sequences from sequencing reads

gggenes

➡️️➡️️⬅️️➡️️ Draw gene arrow maps in ggplot2

NanoPlot

Plotting scripts for long read sequencing data

cellrank

CellRank: dynamics from multi-view single-cell data

higlass

Fast, flexible and extensible genome browser.

cols4all

Colors for all (R package)

cNMF

Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data

pycoQC

pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecaller (Albacore/Guppy)

ggsankey

Make sankey, alluvial and sankey bump plots in ggplot

UCE

UCE is a zero-shot foundation model for single-cell gene expression data

Metabuli

Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.

SATURN

OMArk

RERconverge

Analysis of convergence between organismal traits and DNA/protein sequences

PhyloAcc

PhyloAcc a software to detect the changes of conservation of a genomic region

parnas

Phylogenetic maximum representation sampling: choosing most representative strains or taxa

sceptre

An R package for single-cell CRISPR screen data analysis emphasizing statistical rigor, massive scalability, and ease of use.

donni

machine learning applications for dadi

m6ABasecaller

An m6A-aware basecalling model to detect m6A modifications at single nucleotide resolution in individual reads (Cruciani, Delgado-Tejedor, Pryszcz et al., BioRxiv 2023)

Tutorial_MCMCtree

MCMCtree tutorials

phylokit

Phylogenetics toolkit for the PyData Ecosystem

pyranges_1.x

PyRanges as a DataFrame subclass.

pagan2-msa

PAGAN2 multiple sequence aligner

human_novo_protein_2022

primer-of-evolution

Primer of Evolution