bioinformatics
Repositories (1466)
OhmNet: Representation learning in multi-layer graphs
BANKSY: Spatial Clustering Algorithm that Unifies Cell-Typing and Tissue Domain Segmentation. Python package for spatial transcriptomics analysis.
🍪 SEnsible Step-wise Analysis of DNA MEthylation BeadChips
ChIP-Atlas: Browse and analyze all public ChIP/DNase-seq data on your browser
Protein structure alignment and search algorithm
LAMBDA – the Local Aligner for Massive Biological DatA
🫧🧬 From fragmented assemblies to high-quality bacteriophage genomes
A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category
Tutorial of single-cell RNA-ATAC multiomic sequencing data analysis
A Julia package to analyze protein sequences, structures, and evolutionary information
Snakemake-based workflow for detecting structural variants in genomic data
FlashFry: The rapid CRISPR target site characterization tool
A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data
A C library for handling bigWig files
Scripts, utilities and programs for genomic bioinformatics.
Solutions to assignments of Coursera Specializations - Deep learning, Machine learning, Algorithms & Data Structures, Image Processing and Python For...
:card_index: Retrieve data in genomic intervals with a Python interface for tabix.
:construction_worker: Fasten toolkit, for streaming operations on fastq files
A versatile tool to perform pile-up analysis on Hi-C data in .cool format.
Search ClinicalTrials.gov trials, retrieve study details and results, and match patients to eligible trials via MCP. STDIO or Streamable HTTP.
BBTools: Official suite of fast, multithreaded bioinformatics tools for DNA/RNA analysis. BBMap aligner, BBDuk trimmer, BBMerge, and 90+ other tools....
Fast and flexible ORF finder
Lynn Langit profile
A set of python tools to deal with PDB chemical components definitions for small molecules, taken from the wwPDB Chemical Component Dictionary, uses R...
Structural Bioinformatics is awesome. Throw your textbook in the garbage, light the garbage can on fire, and blend the ashes into your cold brew almon...
Model and predict short DNA sequence features with neural networks
Woltka: a versatile meta'omic data classifier
De novo clustering of long transcript reads into genes
🧬 ManyFold: An efficient and flexible library for training and validating protein folding models
User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
A scalable bacterial genome assembly, annotation and analysis pipeline
Bioinformatic infrastructure libraries
An R Package for Geneset Enrichment Workflows
A fast tool for hybrid genome assembly of long and short reads
A library for generating an interactive SVG visualization of CWL workflows
Command-first ATAC-seq footprinting, motif analysis, and reproducible interactive reports
EDGE is a highly adaptable bioinformatics platform that allows laboratories to quickly analyze and interpret genomic sequence data.
:art: Image processing toolbox for R
A Snakemake workflow and MrBiomics module for performing genomic region set and gene set enrichment analyses using LOLA, GREAT, GSEApy, pycisTarget an...
Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.
NeoDTI: Neural integration of neighbor information from a heterogeneous network for discovering new drug-target interactions
Transcriptomics Visualization R package.
An SKLearn-style toolbox for estimating and analyzing models, distributions, and functions with context-specific parameters.
Merging, Annotation, Validation, and Illustration of Structural variants
Bacterial Isolate Genome Sequence Database (BIGSdb): A platform for gene-by-gene bacterial population annotation and analysis.
Top open source software from the top 50 pharmaceutical companies
From annotated genomes to metabolic screening in large scale microbiotas
fast data structures and algorithms written in Rust, usable from Python.
Implementation of Neural Distance Embeddings for Biological Sequences (NeuroSEED) in PyTorch (NeurIPS 2021)