Discover gersteinlab/GRAM Open Source project

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GRAM: A GeneRAlized Model to predict the molecular effect of a non-coding variant in a cell type-specific manner

ML-Bench

The Official Repo of ML-Bench: Evaluating Large Language Models and Agents for Machine Learning Tasks on Repository-Level Code (https://arxiv.org/abs/2311.09835)

MedAgents

ThermoNet

ThermoNet is a computational method for quantitative prediction of the impact of single-point mutations on protein thermodynamic stability. The core algorithm of ThermoNet is an ensemble of deep 3D convolutional neural networks.

Struc-Bench

BioCoder

SAMChain

MUSIC

MUltiScale enrIchment Calling for ChIP-Seq Datasets

C++

MolLM

A Unified Language Model to Integrate Biomedical Text with 2D and 3D Molecular Representations

Python

GenAI4Drug

aloft

ALOFT, the Annotation Of Loss-of-Function Transcripts, provides extensive functional annotations to loss-of-function variants in the human genome.

Python

MatchedFilter

Prediction of Active Enhancers and Promoters in a Cell type specific manner using shape matching of histone and/or DNase-I hypersensitivity profiles

Python

forest-fire-clustering

A clustering algorithm that can perform internal validation inspired by forest fire dynamics and self-organized criticality

Python

DeepVelo

Jupyter Notebook

starrpeaker

STARRPeaker: STARR-seq peak caller

Python

SVFX

Machine learning framework to quantify pathogenicity of structural variants

Python

siglasso

Optimizing Cancer Mutation Signatures Jointly with Sampling Likelihood

HiC-spector

Spectral and reproducibility analysis of Hi-C contact maps

Julia

LESSeq

Local Event-based analysis of alternative Splicing using RNA-Seq

idash19he

C++

STRESS

FunSeq2

A flexible framework to annotate and prioritize cancer somatic mutations.

Perl

PsychENCODE-DSPN

#DSPN

MATLAB

topicnet

entexBERT

The DNABERT model for ENTEx

Python

OrthoClust

Julia

texp

TeXP is a pipeline to gauge the autonomous transcription level of L1 subfamilies using short read RNA-seq data

Makefile

LARVA

Large-scale Analysis of Recurrent Variants in noncoding Annotations

C++

PeakSeq

Identifying and ranking peak regions in ChIP-Seq experiments

C++

MrTADFinder

a method to identify TADs in Hi-C data

Julia

UMG

A network propagation method to prioritize long tail genes in cancer

Python

RSEQtools

A modular framework to analyze RNA-Seq data using compact and anonymized data summaries.

RADAR

step-back-profiling

mhealthCI

FusionSeq

Identifying fusion transcripts by using paired-end RNA Sequencing

MEDIQA-Chat-2023

MEDIQA-Chat-2023 GersteinLab solution

Jupyter Notebook

papers.gersteinlab.org

decoasthma

Code to reproduce the analyses described in the manuscript, "Approaches for integrating heterogeneous RNA-seq data reveals cross-talk between microbes and genes in asthmatic patients"

HTML

idash22bc

Solution to track 1 of iDASH 2022 secure genome analysis competition

JavaScript

shiny-dim-reduction

This project applies dimensionality reduction to tabular data and generates applications for visualizing the results.

idash19bc

Solution to iDASH'19 challenge track 1

JavaScript

vat

Variant Annotation Tool

PHP

FANCY

Predicting privacy risk of functional genomics data

Jupyter Notebook

retrodup

An integrated retroduplication caller based on 1) exon-exon junction and 2) discordant reads

Perl

chronODE

Jupyter Notebook

HotCommics

Frustration

Python

uORFs

Output files and source code for our project predicting functional upstream open reading frames.

Python

PLIGHT

Privacy Leakage through Inference across Genotypic HMM Trajectories

Python

Public_Documents

A Repository for Gerstein Lab public documents.

Loregic

nimbus

ABCD

Python

TIP

MOAT

Mutations Overburdening Annotations Tool

C++

IQSeq

Isoform quantification from RNA-seq data

dAsthma

scan-atac-sim

SCAN-ATAC Sim is a single-cell ATAC-seq data simulator used to benchmark various single-cell ATAC-seq data analysis methods.

MOBI

idash20FL

Factual_ClinicalSumm

gersteinlab/GRAM

gersteinlab

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