Projects in Awesome Lists by gersteinlab
A curated list of projects in awesome lists by gersteinlab .
https://github.com/gersteinlab/ML-Bench
ML-Bench: Evaluating Large Language Models and Agents for Machine Learning Tasks on Repository-Level Code (https://arxiv.org/abs/2311.09835)
Last synced: 26 Apr 2026
https://github.com/gersteinlab/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)
Last synced: 16 May 2025
https://github.com/gersteinlab/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)
Last synced: 16 Oct 2025
https://github.com/gersteinlab/locagent
Graph-guided agentic framework for code localization
Last synced: 23 Jul 2025
https://github.com/gersteinlab/medagents
llm llm-agent llm-agents medical-application medical-question-answering
Last synced: 09 Apr 2025
https://github.com/gersteinlab/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.
Last synced: 23 Jun 2025
https://github.com/gersteinlab/genai4drug
drug-discovery genai molecule protein
Last synced: 03 Aug 2025
https://github.com/gersteinlab/MedAgentsBench
MedAgentsBench: Benchmarking Thinking Models and Agent Frameworks for Complex Medical Reasoning
Last synced: 11 May 2026
https://github.com/gersteinlab/music
MUltiScale enrIchment Calling for ChIP-Seq Datasets
Last synced: 15 May 2025
https://github.com/gersteinlab/MUSIC
MUltiScale enrIchment Calling for ChIP-Seq Datasets
Last synced: 11 May 2025
https://github.com/gersteinlab/aloft
ALOFT, the Annotation Of Loss-of-Function Transcripts, provides extensive functional annotations to loss-of-function variants in the human genome.
Last synced: 15 May 2025
https://github.com/gersteinlab/matchedfilter
Prediction of Active Enhancers and Promoters in a Cell type specific manner using shape matching of histone and/or DNase-I hypersensitivity profiles
Last synced: 12 Aug 2025
https://github.com/gersteinlab/forest-fire-clustering
A clustering algorithm that can perform internal validation inspired by forest fire dynamics and self-organized criticality
Last synced: 15 May 2025
https://github.com/gersteinlab/starrpeaker
STARRPeaker: STARR-seq peak caller
Last synced: 15 Oct 2025
https://github.com/gersteinlab/psychencode_singlecell_integrative
Integrative Analyses across 388 human brain samples at single-cell resolution
Last synced: 12 Apr 2025
https://github.com/gersteinlab/mollm
A Unified Language Model to Integrate Biomedical Text with 2D and 3D Molecular Representations
Last synced: 02 Apr 2026
https://github.com/gersteinlab/svfx
Machine learning framework to quantify pathogenicity of structural variants
Last synced: 15 May 2025
https://github.com/gersteinlab/hic-spector
Spectral and reproducibility analysis of Hi-C contact maps
Last synced: 02 Jan 2026
https://github.com/gersteinlab/siglasso
Optimizing Cancer Mutation Signatures Jointly with Sampling Likelihood
Last synced: 15 May 2025
https://github.com/gersteinlab/bc-design
BC-Design: A Biochemistry-Aware Framework for High-Precision Inverse Protein Folding
computational-biology inverse-design protein protein-structure protein-surface
Last synced: 01 Aug 2025
https://github.com/gersteinlab/funseq2
A flexible framework to annotate and prioritize cancer somatic mutations.
Last synced: 15 May 2025
https://github.com/gersteinlab/lesseq
Local Event-based analysis of alternative Splicing using RNA-Seq
Last synced: 15 May 2025
https://github.com/gersteinlab/texp
TeXP is a pipeline to gauge the autonomous transcription level of L1 subfamilies using short read RNA-seq data
bioinformatics bioinformatics-pipeline
Last synced: 26 Dec 2025
https://github.com/gersteinlab/larva
Large-scale Analysis of Recurrent Variants in noncoding Annotations
Last synced: 22 Apr 2026
https://github.com/gersteinlab/rseqtools
A modular framework to analyze RNA-Seq data using compact and anonymized data summaries.
Last synced: 21 Apr 2026
https://github.com/gersteinlab/mrtadfinder
a method to identify TADs in Hi-C data
Last synced: 30 Jul 2025
https://github.com/gersteinlab/peakseq
Identifying and ranking peak regions in ChIP-Seq experiments
Last synced: 15 May 2025
https://github.com/gersteinlab/umg
A network propagation method to prioritize long tail genes in cancer
Last synced: 13 Mar 2025
https://github.com/gersteinlab/mimir
[EMNLP 2024] MIMIR: A Streamlined Platform for Personalized Agent Tuning in Domain Expertise https://arxiv.org/abs/2404.04285
Last synced: 14 Oct 2025
https://github.com/gersteinlab/retrodup
An integrated retroduplication caller based on 1) exon-exon junction and 2) discordant reads
Last synced: 20 Apr 2026
https://github.com/gersteinlab/mediqa-chat-2023
MEDIQA-Chat-2023 GersteinLab solution
Last synced: 13 Apr 2026
https://github.com/gersteinlab/shiny-dim-reduction
This project applies dimensionality reduction to tabular data and generates applications for visualizing the results.
Last synced: 05 Jan 2026
https://github.com/gersteinlab/fusionseq
Identifying fusion transcripts by using paired-end RNA Sequencing
Last synced: 04 Jul 2025
https://github.com/gersteinlab/idash19bc
Solution to iDASH'19 challenge track 1
Last synced: 07 Sep 2025
https://github.com/gersteinlab/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"
Last synced: 19 Mar 2026
https://github.com/gersteinlab/gram
GRAM: A GeneRAlized Model to predict the molecular effect of a non-coding variant in a cell type-specific manner
Last synced: 13 Mar 2025
https://github.com/gersteinlab/idash22bc
Solution to track 1 of iDASH 2022 secure genome analysis competition
Last synced: 13 Mar 2025
https://github.com/gersteinlab/fancy
Predicting privacy risk of functional genomics data
Last synced: 28 Apr 2026
https://github.com/gersteinlab/.github
This is the repo for the public organization profile.
Last synced: 12 Feb 2026
https://github.com/gersteinlab/iqseq
Isoform quantification from RNA-seq data
Last synced: 22 Aug 2025
https://github.com/gersteinlab/network-viewer
Network viewer based on Cytoscape Web.
Last synced: 13 Mar 2025
https://github.com/gersteinlab/uorfs
Output files and source code for our project predicting functional upstream open reading frames.
Last synced: 31 Aug 2025
https://github.com/gersteinlab/plight
Privacy Leakage through Inference across Genotypic HMM Trajectories
Last synced: 29 Dec 2025
https://github.com/gersteinlab/public_documents
A Repository for Gerstein Lab public documents.
Last synced: 17 Mar 2026
https://github.com/gersteinlab/chromosomepaintingtool
Chromosome Painting Tool for visualizing signal track density heat-maps of ENTEx experiments.
Last synced: 30 Jan 2026
https://github.com/gersteinlab/thunder
Rob's random collection of mostly RNA-seq tools
Last synced: 13 Mar 2025
https://github.com/gersteinlab/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.
Last synced: 13 Jul 2025
https://github.com/gersteinlab/moat
Mutations Overburdening Annotations Tool
Last synced: 13 Mar 2025
https://github.com/gersteinlab/gersteinlab.github.com
Gerstein Lab Personal Page
Last synced: 28 Feb 2026
https://github.com/gersteinlab/github_howto
How the Gerstein lab can most effectively use Github
Last synced: 06 Apr 2026
https://github.com/gersteinlab/regulatory_targets
Scripts to identify potential target genes of regulatory elements
Last synced: 29 Dec 2025
https://github.com/gersteinlab/pathwaygat
A GAT-based framework integrating multi-layer information with a pathway network
Last synced: 06 Mar 2026
https://github.com/gersteinlab/ngr
Network-based Gene Ranking of Contribution to Cancer [HM]
Last synced: 01 May 2026
https://github.com/gersteinlab/logit-fit
Logistic regression fitting code designed for use with CUDA. Rather than speeding up the running time of a single regression, the code performs the regression in parallel on hundreds of samples.
Last synced: 27 Apr 2026
https://github.com/gersteinlab/scdynamo
Data-driven scRNA-seq Dynamics with Neural Ordinary Differential Equations
Last synced: 16 Jun 2025
https://github.com/gersteinlab/annotation-k-mer-extractor
Using sliding window to extract k-mers for annotation (specfically exons) in GTF format
Last synced: 02 Jul 2025