A Python toolkit for subcellular analysis of spatial transcriptomics data

Generate embeddings from large-scale graph-structured data.

Gene set variation analysis

Single Cell RNA-seq UMI Filtering Facilitator

Medical Image Segmentation using Squeeze-and-Expansion Transformers

Codes and models for the paper "Learning Unknown from Correlations: Graph Neural Network for Inter-novel-protein Interaction Prediction".

A better, faster way to count guides in CRISPR screens.

SCREE (Single-cell CRISPR screen data analysEs and perturbation modEling) is a workflow to perform quality control and analyses of multimodal single-cell CRISPR screen datasets.

Reference-free cell-type deconvolution of multi-cellular spatially resolved transcriptomics data

Multi-subject Single Cell Deconvolution

De-Novo Repeat Discovery Tool

Web-based bioinformatics software for correlating genome-wide DNA methylation and gene expression

Genomic Association Tester

R package implementation of Milo for testing for differential abundance in KNN graphs

scPerturb: A resource and a python/R tool for single-cell perturbation data

Near-optimal RNA-Seq quantification

VoxHunt: Resolving human brain organoid heterogeneity through single-cell genomic comparison to spatial brain maps

A repository for the design and analysis of pooled single cell RNA-seq perturbation experiments.

Multiome GRN inference.

A tool to map bisulfite converted sequence reads and determine cytosine methylation states

Shiny Interactive Web Apps for Single-Cell Data

🎄Visualization and annotation of phylogenetic trees

Extract 3D contacts (.pairs) from sequencing alignments

Micro-C QC and data analysis

Transcription Factor Enrichment Analysis

Joint normalization of multiple Hi-C matrices, visualization and detection of differential chromatin interactions, supporting covariates.