Introduction to data visualization with R

python module to plot beautiful and highly customizable genome browser tracks

Prediction Performance Metrics

Unix, R and python tools for genomics and data science

A Deep Learning-Based Model for the integration, cross-dataset cross-modality generation, self augmentation and matched multi-omics simulation of single-cell multi-omics data. Our model excels at m…

Code for reproducing the figures presented in the manuscript 'Identification of genomic enhancers through spatial integration of single-cell transcriptomics and epigenomics' (Bravo et al., 2020)

Karate Club: An API Oriented Open-source Python Framework for Unsupervised Learning on Graphs (CIKM 2020)

Papers of Neural Topic Models (NTMs)

A continually expanding collection of RNA-seq tools

Turn your data frame into a tableau style drag and drop UI interface to build visualization in R.

Code for SpecNet2

R/Bioconductor package for working with 10x scATACseq data

Co-accessibility network from single-cell ATAC-seq data. Python code, based on Cicero package (R).

Time series forecasting with PyTorch

A method for analyzing scATAC-seq experiments.

Awesome Deep Graph Clustering is a collection of SOTA, novel deep graph clustering methods (papers, codes, and datasets).

An open-source framework for self-supervised recommender systems.

Unified access to several second-generation deconvolution methods

A curated list of papers on large-scale graph learning.

BENchmark inteGrAtion strategies for cross-species anaLysis of single cell RNA sequencing data

R Weekly

Functions to Create Publication-Quality Plots

Bulk (CP/GZ) and single-cell Iso-Seq in the developing human brain

A list of interesting genome browser or genome-browser-like implementations

[Mamba-Survey-2024] Paper list for State-Space-Model/Mamba and it's Applications

Awesome Papers related to Mamba.

Mamba SSM architecture

PhyloVelo, Phylogeny-based transcriptomic velocity of single cells