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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 DatasetsMolLM
A Unified Language Model to Integrate Biomedical Text with 2D and 3D Molecular RepresentationsGenAI4Drug
aloft
ALOFT, the Annotation Of Loss-of-Function Transcripts, provides extensive functional annotations to loss-of-function variants in the human genome.MatchedFilter
Prediction of Active Enhancers and Promoters in a Cell type specific manner using shape matching of histone and/or DNase-I hypersensitivity profilesforest-fire-clustering
A clustering algorithm that can perform internal validation inspired by forest fire dynamics and self-organized criticalityDeepVelo
starrpeaker
STARRPeaker: STARR-seq peak callerSVFX
Machine learning framework to quantify pathogenicity of structural variantssiglasso
Optimizing Cancer Mutation Signatures Jointly with Sampling LikelihoodHiC-spector
Spectral and reproducibility analysis of Hi-C contact mapsLESSeq
Local Event-based analysis of alternative Splicing using RNA-Seqidash19he
STRESS
FunSeq2
A flexible framework to annotate and prioritize cancer somatic mutations.PsychENCODE-DSPN
#DSPNtopicnet
entexBERT
The DNABERT model for ENTExOrthoClust
texp
TeXP is a pipeline to gauge the autonomous transcription level of L1 subfamilies using short read RNA-seq dataLARVA
Large-scale Analysis of Recurrent Variants in noncoding AnnotationsPeakSeq
Identifying and ranking peak regions in ChIP-Seq experimentsMrTADFinder
a method to identify TADs in Hi-C dataUMG
A network propagation method to prioritize long tail genes in cancerRSEQtools
A modular framework to analyze RNA-Seq data using compact and anonymized data summaries.RADAR
RADAR source codemhealthCI
FusionSeq
Identifying fusion transcripts by using paired-end RNA SequencingMEDIQA-Chat-2023
MEDIQA-Chat-2023 GersteinLab solutionpapers.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"idash22bc
Solution to track 1 of iDASH 2022 secure genome analysis competitionshiny-dim-reduction
This project applies dimensionality reduction to tabular data and generates applications for visualizing the results.idash19bc
Solution to iDASH'19 challenge track 1step-back-profiling
vat
Variant Annotation ToolFANCY
Predicting privacy risk of functional genomics dataretrodup
An integrated retroduplication caller based on 1) exon-exon junction and 2) discordant readschronODE
HotCommics
Frustration
PLIGHT
Privacy Leakage through Inference across Genotypic HMM TrajectoriesPublic_Documents
A Repository for Gerstein Lab public documents.Loregic
nimbus
ABCD
TIP
TIPMOAT
Mutations Overburdening Annotations ToolIQSeq
Isoform quantification from RNA-seq datadAsthma
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
GRAM
GRAM: A GeneRAlized Model to predict the molecular effect of a non-coding variant in a cell type-specific manneridash20FL
Factual_ClinicalSumm
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