bioinformatics
Repositories (1438)
A C library for handling bigWig files
A genome diagram generator for microbes and organelles
Solutions to assignments of Coursera Specializations - Deep learning, Machine learning, Algorithms & Data Structures, Image Processing and Python For...
Protein structure alignment and search algorithm
Intuitive guide to multi-omics integration with toy examples: supervised latent components (DIABLO), unsupervised shared/partial/unique structure (DIV...
Model and predict short DNA sequence features with neural networks
A library for generating an interactive SVG visualization of CWL workflows
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...
User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
An R Package for Geneset Enrichment Workflows
Tutorial of single-cell RNA-ATAC multiomic sequencing data analysis
BANKSY: Spatial Clustering Algorithm that Unifies Cell-Typing and Tissue Domain Segmentation. Python package for spatial transcriptomics analysis.
Bioinformatic infrastructure libraries
Woltka: a versatile meta'omic data classifier
A fast tool for hybrid genome assembly of long and short reads
EDGE is a highly adaptable bioinformatics platform that allows laboratories to quickly analyze and interpret genomic sequence data.
NeoDTI: Neural integration of neighbor information from a heterogeneous network for discovering new drug-target interactions
An SKLearn-style toolbox for estimating and analyzing models, distributions, and functions with context-specific parameters.
A scalable bacterial genome assembly, annotation and analysis pipeline
:art: Image processing toolbox for R
Merging, Annotation, Validation, and Illustration of Structural variants
A Snakemake workflow and MrBiomics module for performing genomic region set and gene set enrichment analyses using LOLA, GREAT, GSEApy, pycisTarget an...
Transcriptomics Visualization R package.
🦠🧬🧑‍💻📇 Microbial genomes-to-report pipeline
đź“› A Python package for using ontologies, terminologies, and biomedical nomenclatures
Bacterial Isolate Genome Sequence Database (BIGSdb): A platform for gene-by-gene bacterial population annotation and analysis.
Efficient implementations of Needleman-Wunsch and other sequence alignment algorithms written in Rust with Python bindings via PyO3.
Provides access to complex Bioinformatics software (even BioLinux!) in just one command.
Analysis pipelines for genomic sequencing data
dcHiC: Differential compartment analysis for Hi-C datasets
Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.
Fast and precise comparison of genomes and metagenomes (in the order of terabytes) on a typical personal laptop
Lightweight converter between hic and cool contact matrices.
High-performance error correction for Illumina resequencing data
A WGS de novo assembler based on the FMD-index for large genomes
Implementation of Neural Distance Embeddings for Biological Sequences (NeuroSEED) in PyTorch (NeurIPS 2021)
Monitor computational workflows in real time
The MPI Bioinformatics Toolkit
ClassifyCNV: a tool for clinical annotation of copy-number variants
Ontology Tutorial
De novo clustering of long transcript reads into genes
An ultra-high-performance protein-protein docking for heterogeneous supercomputers
Python3 scripts to manipulate FASTA and FASTQ files
Top open source software from the top 50 pharmaceutical companies
Tibanna helps you run your genomic pipelines on Amazon cloud (AWS). It is used by the 4DN DCIC (4D Nucleome Data Coordination and Integration Center)...
An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
Incremental construction of FM-index for DNA sequences
Standalone C library for assembling Illumina short reads in small regions