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antiformer

Knowledge graph enhanced LLM for binding affinity prediction

bimm

Uncovering the dynamic effects of DEX treatment on lung cancer by integrating bioinformatic inference and multiscale modeling of scRNA-seq and proteomics data

biscuit_singlecell_imm_icml_2016

R Codebase for BISCUIT: Infinite Mixture Model to cluster and impute single cells.

brainmapr

R package to infer spatial location of neuronal subpopulations within the developing mouse brain by integrating single-cell RNA-seq data with in situ RNA patterns from the Allen Developing Mouse Brain Atlas

brcarepred

brmet

Single cell sequencing reveals the landscape of the brain metastatic microenvironment

conics

CONICS: COpy-Number analysis In single-Cell RNA-Sequencing

dstg

Deconvoluting Spatial Transcriptomics Data through Graph-based Artificial Intelligence

ebcall

an empirical Bayesian framework for mutation detection from cancer genome sequencing data

hggep

Gene Expression Prediction from Histology Images via Hypergraph Neural Networks

labs

Rmd source files for the HarvardX series PH525x

machinelearning

Machine learning resources

methylation-recipes

Scripts related to 450k and EPIC data analysis

miracum-pipe

Whole exome sequencing pipeline including advanced variant annotation features and automated PDF reporting.

nextgenseq_pipeline

Exome/Capture/RNASeq Pipeline Implementation using snakemake

prmlt

Matlab code for machine learning algorithms in book PRML

python-cheatsheet

Comprehensive Python Cheatsheet

rna_mutect_1.0-1

rnaseq-pipeline

Description of the different step in Pipeline RNAseq Single End. From fastq to count tables.

rnatools

Functions for processing RNA-seq data using multiple methods. Provides consistent interfaces for normalisation, testing, visualisation etc.

sccca

scCCA: Leveraging multiple single cell datasets through CCA algorithm

sceqtl

scgcn

scGCN is a graph convolutional networks algorithm for knowledge transfer in single cell omics

sclm

Automatic detection of consensus gene clusters across multiple single-cell datasets

scperb

scPerb: predict single-cell perturbation via style transfer-based variational autoencoder

seqc

Single-Cell Sequencing Quality Control and Processing Software

sigra

Single-cell spatial elucidation through image-augmented graph transformer

smgr

SMGR: a joint statistical method for integrative analysis of single-cell multi-omics data

songlab

spaci

Deciphering spatial cellular communications through adaptive graph model