timoast

AMULET

A count based method for detecting doublets from single nucleus ATAC-seq (snATAC-seq) data.

scifiRNA-seq_publication

The million-scale method for single-cell analysis

vireo

Demultiplexing pooled scRNA-seq data with or without genotype reference

cellsnp-lite

Efficient genotyping bi-allelic SNPs on single cells

deep_learning_papers

A place to collect papers that are related to deep learning and computational biology

bamtofastq

Convert 10x BAM files to the original FASTQs compatible with 10x pipelines

The-world-of-faculty

resources for faculty

paletteer

🎨🎨🎨 Collection of most color palettes in a single R package

scATAC-benchmarking

Benchmarking computational single cell ATAC-seq methods

docker-cheat-sheet

Docker Cheat Sheet

deep-review

A collaboratively written review paper on deep learning, genomics, and precision medicine

awesome-deepbio

A curated list of awesome deep learning applications in the field of computational biology

fastISM

In-silico Saturation Mutagenesis implementation with 10x or more speedup for certain architectures.

AI-TAC

extendr

R extension library for rust designed to be familiar to R users.

sampleproject

A sample project that exists for PyPUG's "Tutorial on Packaging and Distributing Projects"

captum

Model interpretability and understanding for PyTorch

scico

Palettes for R based on the Scientific Colour-Maps

mamba

The Fast Cross-Platform Package Manager

pytorch-lightning

Pretrain, finetune ANY AI model of ANY size on multiple GPUs, TPUs with zero code changes.

optuna

A hyperparameter optimization framework

signac-kit

Fast wrapper around signac atac-seq processing workflow.

models

Model zoo for genomics

kipoi

Kipoi's model zoo API

kipoiseq

Standard set of data-loaders for training and making predictions for DNA sequence-based models.

monocle3

awesome-ml-courses

Awesome free machine learning and AI courses with video lectures.

seurat-disk

Interfaces for HDF5-based Single Cell File Formats

oocPCA

Out-of-Core Principal Component Analysis

Genrich

Detecting sites of genomic enrichment