yuhsinhsieh-josch

ArchRCells

ArchR Metacell creation from SEACells

multiSAP

Multiome Sequencing Analysis Pipeline

oor_design_reproducibility

oh-my-bash

A delightful community-driven framework for managing your bash configuration, and an auto-update tool so that makes it easy to keep up with the latest updates from the community.

BI-BE-CS-183-2023

Introduction to Computational Biology and Bioinformatics Course at Caltech, 2023

2023

oor_benchmark

A sandbox for benchmarking detection of out-of-reference cells in single-cell genomics data

probai-2023

Materials of the Nordic Probabilistic AI School 2023.

multigrate

Multigrate: multiomic data integration for single-cell genomics

chrombpnet

Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)

PerturbDecode

An end-to-end computational pipeline for large Perturb-seq screens

scGPT

chromograph

Camiel's scATAC-seq analysis pipeline

DELAY

Depicting pseudotime-lagged causality for accurate gene-regulatory inference

scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data

mrvi_archive

Multi-resolution Variational Inference

DAseq

multimodal-vae-public

A PyTorch implementation of "Multimodal Generative Models for Scalable Weakly-Supervised Learning" (https://arxiv.org/abs/1802.05335)

multiSAP

Multiome Sequencing Analysis Pipeline

MoMAColors

Color Schemes based around artwork and the Museum of Modern Art.

scg_lib_structs

Collections of library structure and sequence of popular single cell genomic methods

muscat

Multi-sample multi-group scRNA-seq analysis tools

decoupleR

R package to infer biological activities from omics data using a collection of methods.

cplvm

Contrastive Poisson latent variable models (CPLVMs)

pcpca

Probabilistic contrastive principal component analysis (PCPCA)

cNMF

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

contrastiveVI

notebook-copilot

From Thoughts to Well-Crafted Jupyter Notebook at Record-Speed

MAST

Tools and methods for analysis of single cell assay data in R

scanpro