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This deep learning model is designed for ECG image classification, fine-tuned using ResNet-50. It can classify ECG images into different categories to assist in heart disease detection.

The Lheuristic package identifies scatterpots that follow and L-shaped, negative distribution. It can be used to identify genes regulated by methylation by integration of an expression and a methylation array. The package uses two different methods to detect expression and methyaltion L- shapped scatterplots. The parameters can be changed to detect other scatterplot patterns.

tLOH, or transcriptomicsLOH, assesses evidence for loss of heterozygosity (LOH) in pre-processed spatial transcriptomics data. This tool requires spatial transcriptomics cluster and allele count information at likely heterozygous single-nucleotide polymorphism (SNP) positions in VCF format. Bayes factors are calculated at each SNP to determine likelihood of potential loss of heterozygosity event. Two plotting functions are included to visualize allele fraction and aggregated Bayes factor per chromosome. Data generated with the 10X Genomics Visium Spatial Gene Expression platform must be pre-processed to obtain an individual sample VCF with columns for each cluster. Required fields are allele depth (AD) with counts for reference/alternative alleles and read depth (DP).

Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis.

Functions for the projection of data into the spaces defined by PCA, CoGAPS, NMF, correlation, and clustering.

This package provides a method to refit and correct the diploid region in copy number profiles. It uses a clustering algorithm to identify pathology-specific normal (diploid) chromosomes and then use their copy number signal to refit the whole profile. The package is composed by three functions: DRrefit (the main function), ComputeNormalChromosome and PlotCluster.

Python wrapper for [bedtools](https://github.com/arq5x/bedtools).

A pipeline for the analysis of GRO-seq data.

Diabetica: Adapting Large Language Model to Enhance Multiple Medical Tasks in Diabetes Care and Management

TFBSTools is a package for the analysis and manipulation of transcription factor binding sites. It includes matrices conversion between Position Frequency Matirx (PFM), Position Weight Matirx (PWM) and Information Content Matrix (ICM). It can also scan putative TFBS from sequence/alignment, query JASPAR database and provides a wrapper of de novo motif discovery software.

This tutorial aims to illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks (biobb) REST API. The particular example used is the Lysozyme protein (PDB code 1AKI).

An SCVI model and minified AnnData of the Tahoe-100M dataset from Vevo Tx.

A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files).

PPTStab: Prediction and Designing of thermostable proteins with a desired melting temperature

Base-resolution copy number analysis of viral genome. Utilizes base-resolution read depth data over viral genome to find copy number segments with two-dimensional segmentation approach. Provides publish-ready figures, including histograms of read depths, coverage line plots over viral genome annotated with copy number change events and viral genes, and heatmaps showing multiple types of data with integrative clustering of samples.

Simple visualizations of alignments of DNA or AA sequences as well as arbitrary strings. Compatible with Biostrings and ggplot2. The plots are fully customizable using ggplot2 modifiers such as theme().

INDUS-Retriever-small (previously nasa-smd-ibm-st.38m) is a Bi-encoder sentence transformer model, that is fine-tuned from distilled version of nasa-smd-ibm-v0.1 encoder model. it is a smaller version of nasa-smd-ibm-st with better performance, using fewer parameters (shown below).

Save MultiAssayExperiments to h5mu files supported by muon and mudata. Muon is a Python framework for multimodal omics data analysis. It uses an HDF5-based format for data storage.

If you are unsure how to use GGUF files, refer to one of TheBloke's READMEs for more details, including on how to concatenate multi-part files.

Neural optical understanding for academic documents, transforms scientific PDFs to Markdown with mathematical formula support

Generate comprehensive reviews from arXiv papers and convert to blog posts

Microsoft's AI-powered ab initio biomolecular dynamics simulation achieving quantum-mechanical accuracy for proteins with 10,000+ atoms, orders of magnitude faster than DFT using protein fragmentation and ML force fields (Nature 2024)

A database system designed to store, organize, and manage large-scale nucleotide sequencing read data (like PacBio reads) for the Dazzler genome assembler

This package defines a custom landing page for an iSEE app interfacing with the Bioconductor ExperimentHub. The landing page allows users to browse the ExperimentHub, select a data set, download and cache it, and import it directly into a Bioconductor iSEE app.

Versatile multi-temporal geospatial foundation model for Earth observation, built on a ViT-based masked autoencoder with 3D spatiotemporal patch embeddings and geolocation/temporal metadata encoding; pretrained on 4.2M global time-series samples from NASA's Harmonized Landsat and Sentinel-2 archive at 30m resolution, with 300M/600M parameter variants and fine-tuning configs for flood detection, wildfire scar, landslide detection, crop segmentation, land cover, and biomass estimation (258+ stars, MIT License)

Equivariant graph attention Transformer (ICLR2023)

The eiR package provides utilities for accelerated structure similarity searching of very large small molecule data sets using an embedding and indexing approach.

한국어 모델을 이용한 SapBERT(Self-alignment pretraining for BERT)입니다. 한·영 의료 용어 사전인 KOSTOM을 사용해 한국어 용어와 영어 용어를 정렬했습니다. 참고: SapBERT, Original Code

A controlled vocabulary to support the study of transcription in the developing mouse brain

A controlled vocabulary to support the study of transcription in the human brain

This is the base model of GenomeOcean-4B. It is trained with Causal Language Modeling (CLM) and uses a BPE tokenizer with 4096 tokens. It supports a maximum sequence length of 10240 tokens (~50kbp).

A toolbox for sparse contrastive principal component analysis (scPCA) of high-dimensional biological data. scPCA combines the stability and interpretability of sparse PCA with contrastive PCA's ability to disentangle biological signal from unwanted variation through the use of control data. Also implements and extends cPCA.

A terminology for the skills necessary to make data FAIR and to keep it FAIR.

Extension of ProteinMPNN for protein sequence design in the context of small-molecule ligands, metal ions, and nucleic acids, enabling binding site engineering and co-factor redesign (Baker Lab)

A system for rapidly aligning entire genomes, whether in complete or draft form.

Physics-AI hybrid modeling for fine-grained weather forecasting (NeurIPS'24)

An easy to use tool that can compare splicing events in tumor and normal tissue samples using either a user generated matrix, or data from The Cancer Genome Atlas (TCGA). This package generates a matrix of splicing outliers that are significantly over or underexpressed in tumors samples compared to normal denoted by chromosome location. The package also will calculate the splicing burden in each tumor and characterize the types of splicing events that occur.

Comprehensive survey of foundation models for weather and climate data understanding

This package contains R functions to predict biological variables to from placnetal DNA methylation data generated from infinium arrays. This includes inferring ethnicity/ancestry, gestational age, and cell composition from placental DNA methylation array (450k/850k) data.

Geometric deep learning model predicting transcriptional outcomes of novel single- and multi-gene perturbations using gene–gene knowledge graphs, 40% higher precision than prior methods on combinatorial perturbation prediction (Stanford, Nature Biotechnology 2024)

clevRvis provides a set of visualization techniques for clonal evolution. These include shark plots, dolphin plots and plaice plots. Algorithms for time point interpolation as well as therapy effect estimation are provided. Phylogeny-aware color coding is implemented. A shiny-app for generating plots interactively is additionally provided.

# GPN trained on Arabidopsis thaliana and 7 other Brassicales See https://github.com/songlab-cal/gpn for more details.

FeatSeekR performs unsupervised feature selection using replicated measurements. It iteratively selects features with the highest reproducibility across replicates, after projecting out those dimensions from the data that are spanned by the previously selected features. The selected a set of features has a high replicate reproducibility and a high degree of uniqueness.

LLM for scientific research papers

Open-source medical large language model for complex clinical reasoning, extending the o1 long-chain-of-thought paradigm to biomedical question answering and diagnostic inference (FreedomIntelligence, 1.3K+ stars)