wgsim

awesome-deep-learning-single-cell-papers

ProteinFlow

Versatile computational pipeline for processing protein structure data for deep learning applications.

TopPR

NeurIPS 2023 - TopP&R: Robust Support Estimation Approach for Evaluating Fidelity and Diversity in Generative Models Official Code

trackViewer

A bioconductor package with minimalist design for drawing elegant tracks or lollipop plot

lollipops

Lollipop-style mutation diagrams for annotating genetic variations.

XAI-for-bioinformatics

Explainable AI for Bioinformatics

DNA-Diffusion

🧬 Generative modeling of regulatory DNA sequences with diffusion probabilistic models 💨

ChemBioMultimodalAutoencoders

a package for streamlined multidomain data integration and translation based on cross-modal autoencoders architectures

RNA-seq

Step-by-step analysis pipeline for RNA-seq data

dance

DANCE: a deep learning library and benchmark platform for single-cell analysis

ktplotspy

Python library for plotting Cellphonedb results. Ported from ktplots R package.

RoseTTAFold

This package contains deep learning models and related scripts for RoseTTAFold

AlphaPulldown

scsnv

scSNV Mapping tool for 10X Single Cell Data

sra-tools

SRA Tools

rpy2

Interface to use R from Python

pyreadr

Python package to read and write R RData and Rds files into/from pandas dataframes. No R or other external dependencies required.

mousipy

Translates an AnnData object with mouse gene symbols into one with human gene symbols by mapping orthologs from biomart.

infercnvpy

Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.

CellChat

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data

CellphoneDB

CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.

alphafold

Open source code for AlphaFold.

conda-stage

conda-stage: Stage a Conda Environment on Local Disk

py4cytoscape

Python library for calling Cytoscape Automation via CyREST

keggtools

Library for KEGG pathway enrichment analysis

infercnv

Inferring CNV from Single-Cell RNA-Seq

stackview

Interactive image stack viewing in jupyter notebooks based on ipycanvas and ipywidgets