bioinformatics
Repositories (1500)
EDGE is a highly adaptable bioinformatics platform that allows laboratories to quickly analyze and interpret genomic sequence data.
An R Package for Geneset Enrichment Workflows
NeoDTI: Neural integration of neighbor information from a heterogeneous network for discovering new drug-target interactions
A scalable bacterial genome assembly, annotation and analysis pipeline
A library for generating an interactive SVG visualization of CWL workflows
A fast tool for hybrid genome assembly of long and short reads
Bacterial Isolate Genome Sequence Database (BIGSdb): A platform for gene-by-gene bacterial population annotation and analysis.
Single-cell spatial omics analysis that makes you happy!
:art: Image processing toolbox for R
From annotated genomes to metabolic screening in large scale microbiotas
đź“› A Python package for using ontologies, terminologies, and biomedical nomenclatures
A Snakemake workflow and MrBiomics module for performing genomic region set and gene set enrichment analyses using LOLA, GREAT, GSEApy, pycisTarget an...
Top open source software from the top 50 pharmaceutical companies
242 evaluated academic Claude/agent skills across 18 research domains — bioinformatics, cheminformatics, data science, databases, clinical, social sci...
Merging, Annotation, Validation, and Illustration of Structural variants
:golf: GO-terms Semantic Similarity Measures
Monitor computational workflows in real time
ClassifyCNV: a tool for clinical annotation of copy-number variants
Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes
An SKLearn-style toolbox for estimating and analyzing models, distributions, and functions with context-specific parameters.
A Nextflow workflow to generate lift over files for any pair of genomes
fast data structures and algorithms written in Rust, usable from Python.
Provides access to complex Bioinformatics software (even BioLinux!) in just one command.
High-performance error correction for Illumina resequencing data
Fast and precise comparison of genomes and metagenomes (in the order of terabytes) on a typical personal laptop
Implementation of Neural Distance Embeddings for Biological Sequences (NeuroSEED) in PyTorch (NeurIPS 2021)
Efficient implementations of Needleman-Wunsch and other sequence alignment algorithms written in Rust with Python bindings via PyO3.
Transcriptomics Visualization R package.
⚡🦠🧬📇 Rapid microbial genomes-to-report pipeline
Bioinformatics web-platform visualisation dashboard creation
A WGS de novo assembler based on the FMD-index for large genomes
Analysis pipelines for genomic sequencing data
Bayesian MCMC matrix factorization algorithm
The MPI Bioinformatics Toolkit
Lightweight converter between hic and cool contact matrices.
Genomics data visualization in Python by using matplotlib.
An ultra-high-performance protein-protein docking for heterogeneous supercomputers
dcHiC: Differential compartment analysis for Hi-C datasets
Statistical approach for removing unwanted variation from multiple single-cell datasets
Portable solution to generate genome alignment chains using lastz
A fast, feature rich multiple sequence alignment browser for the terminal.
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.
Ontology Tutorial
Python3 scripts to manipulate FASTA and FASTQ files
Universal Transcript Archive: comprehensive genome-transcript alignments; multiple transcript sources, versions, and alignment methods; available as a...
zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)
Volcano plots for differential expression in R. Reads DESeq2, edgeR and limma output directly; highlight genes of interest and compose gene tables wit...
NEAT (NExt-generation Analysis Toolkit) simulates next-gen sequencing reads and can learn simulation parameters from real data.