ZainulArifin1

vespa

VESPA (Virtual Enrichment-based Signaling Protein-activity Analysis) algorithm

sign

SIGN: Scalable Inception Graph Network

graph-neural-pde

Graph Neural PDEs

dgl

Python package built to ease deep learning on graph, on top of existing DL frameworks.

HLCA

ClueR

Cluster Evaluation R package (ClueR) for detecting key signaling events from time-series phosphoproteomics data

ShinyCell

Shiny Interactive Web Apps for Single-Cell Data

BIONIC

Biological Network Integration using Convolutions

MOON_example

cosmosR

COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.

CollecTRI

Gene regulatory network containing signed transcription factor-target gene interactions

ColabFold

Making Protein folding accessible to all!

Inferring-and-Visualizing-RNA-Velocity-in-Bulk-RNA-SEQ

Analysis steps to calculate RNA Velocity in Bulk RNA-Seq samples. Step by Step Guide.

KSP-PUEL

Positive-unlabeled ensemble learning for kinase substrate prediction from dynamic phosphoproteomics data

corral

Dimensionality reduction and batch integration methods for single cell data

MCFA

SEACR

SEACR: Sparse Enrichment Analysis for CUT&RUN

scRNAseq-analysis-notes

scRNAseq analysis notes from Ming Tang

ConsensusTME

ConsensusTME Gene Sets and R Script

scGPT

SnapATAC

Analysis Pipeline for Single Cell ATAC-seq

Interactive-3D-Plotting-in-Seurat-3.0.0

This repository contains R code, with which you can create 3D UMAP and tSNE plots of Seurat analyzed scRNAseq data

PySR

High-Performance Symbolic Regression in Python and Julia

fgbio

Tools for working with genomic and high throughput sequencing data.

AutoGPT

AutoGPT is the vision of accessible AI for everyone, to use and to build on. Our mission is to provide the tools, so that you can focus on what matters.

protanar

PROTeomics ANAlysis in R

CCI

Evaluation of cell-cell interaction methods by integrating single-cell RNA sequencing data with spatial information

metacells

Metacells - Single-cell RNA Sequencing Analysis

Longhack2023-iNET

Longhack2023