XiaoTaoWang

open-interpreter

A natural language interface for computers

segment-anything

The repository provides code for running inference with the SegmentAnything Model (SAM), links for downloading the trained model checkpoints, and example notebooks that show how to use the model.

Anima

33B Chinese LLM, DPO QLORA, 100K context, AirLLM 70B inference with single 4GB GPU

lion-pytorch

🦁 Lion, new optimizer discovered by Google Brain using genetic algorithms that is purportedly better than Adam(w), in Pytorch

mpire

A Python package for easy multiprocessing, but faster than multiprocessing

vg

tools for working with genome variation graphs

cellranger

10x Genomics Single Cell Analysis

PyMIC

Giotto

Spatial omics analysis toolbox

sgkit

Scalable genetics toolkit

SnapATAC2

Single-cell epigenomics analysis tools

CNVpytor

a python extension of CNVnator -- a tool for CNV analysis from depth-of-coverage by mapped reads

agc

Assembled Genomes Compressor

seq2science

Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.

dictys

Context specific and dynamic gene regulatory network reconstruction and analysis

wgatools

Whole Genome Alignment Tools

Gviz

This is the Gviz development repository. Gviz plots data and annotation information along genomic coordinates.

borzoi

RNA-seq prediction with deep convolutional neural networks.

awesome-pangenomes

A list of software for pangenomics

gia

gia: Genomic Interval Arithmetic

DeepSTARR

Deep learning model built to quantitatively predict the activities of developmental and housekeeping enhancers from DNA sequence in Drosophila melanogaster S2 cells

bedrs

bedtools-like functionality for interval sets in rust

DNN-Genealogy

An visual summary of representative DNNs and their evolutionary relationships

clean

A nextflow pipeline for decontamination of short reads, long reads and contigs

PySNAIL

Smooth-quantile Normalization Adaptation for Inference of co-expression Links

HiCrayon

Web-Application for the cross-visualization of HiC and ChIP-seq data.

allo

Allo: a multi-mapped read rescue strategy for gene regulatory analyses

eNet

KGGSEE

KGGSEE: A biological Knowledge-based mining platform for Genomic and Genetic association Summary statistics using gEne Expression

Fun

Algorithm to identify replication fountains