shobhitagrawal1

alphafold3

AlphaFold 3 inference pipeline.

spateo-release

Spatiotemporal modeling of spatial transcriptomics

scTab

GraphPCA

a fast dimension reduction algorithm for spatial transcriptomics data

optimizers

For optimization algorithm research and development.

adopt

Official Implementation of "ADOPT: Modified Adam Can Converge with Any β2 with the Optimal Rate"

mcBERT

ig.degree.betweenness

Smith-Pittman Community Detection Algorithm for 'igraph' Objects (2024) in R

Sanity

Filtering of Poison noise on a single-cell RNA-seq UMI count matrix

Average_samples_mean_and_variance

Compute the average of multiple samples taking into account their individual mean and variance

nicheformer

Repository for Nicheformer: a foundation model for single-cell and spatial omics

ImbalancedLearningForSingleCellFoundationModels

Code for the benchmarking single-cell foundation models (scGPT, scBERT, and Geneformer) for cell-type annotation task using skewed single-cell cell-type distribution data.

rastermap

a visualization method for neural data

LabelCorrection

Python code for cross-condition label refinement in single-cell data with HiDDEN

genular-database

Genular: An Integrated Platform for Defining Cellular Identity and Function through Single-Cell Gene Expression and Multi-Domain Biological Data

genular

:exclamation: This is a read-only mirror of the CRAN R package repository. genular — 'Genular' Database API. Homepage: https://github.com/atomiclaboratory/genular-database, <https://genular.atomic-lab.org> Report bugs for this package: https://github.com/atomiclaboratory/genular-database/issues

TxGNN

TxGNN: Zero-shot prediction of therapeutic use with geometric deep learning and clinician centered design

boda2

Computational Optimization of DNA Activity (CODA)

lorna-manuscript

LoRNA-SH: A long-context RNA foundation model for predicting transcriptome architecture. Pre-processing and downstream analysis scripts.

p-ClustVal

CellWhisperer

CellWhisperer bridges the gap between transcriptomics data and natural language, enabling intuitive interaction with scRNA-seq datasets

scPRINT

single cell foundation model for Gene network inference and more

CellTrek

cell_type_mapper

Repository for storing prototype functionality implementations for the BKP

swarm

Educational framework exploring ergonomic, lightweight multi-agent orchestration. Managed by OpenAI Solution team.

BEYOND_DLPFC

Cellular dynamics across aged human brains uncover a multicellular cascade leading to Alzheimer’s disease

MultiomeBenchmarking

bioicons

A library of free open source icons for science illustrations in biology and chemistry

GeNA

Genotype-Neighborhood Associations: A tool for identifying genetic variant associations to the abundance of cell states in single-cell datasets

SciAgentsDiscovery