bioinformatics
Repositories (1438)
A collection of reusable WDL tasks. Category:Other
Calculation of interatomic interactions in molecular structures
Package for processing and analyzing glycans and their role in biology.
ClairS-TO - a deep-learning method for tumor-only somatic variant calling
📚书：R语言零基础入门
CASSIA: A Multi-Agent LLM-Based Single-Cell Cell Type Annotation Framework
a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference
TypeDB Bio: Biomedical Knowledge Graph
Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).
RNA modifications detection from Nanopore dRNA-Seq data
GO enrichment with python -- pandas meets networkx
List of tools and resources related to the 10x Genomics GEMCode/Chromium system
Bioinformatics tool to find integrons in bacterial genomes
MCP server for the NCBI E-utilities API. Search PubMed, fetch article metadata and full text, generate citations, explore MeSH terms, and discover rel...
A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment
Massively parallel phylogenetic placement of genetic sequences
The START App: R Shiny Transcriptome Analysis Resource Tool
Universal and efficient structure-based core gene phylogeny with Foldseek and ProstT5
:dart: Human transcription factor target genes from 6 databases in convenient R format.
Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.
Python package and CLI for whole-genome duplication related analyses. **This package is deprecated in favor of** https://github.com/heche-psb/wgd.
Yet Another Chimeric Read Detector
biotoolsregistry: discovery portal for bioinformatics
vcfdist: Accurately benchmarking phased variant calls
PyMod 3 - sequence similarity searches, multiple sequence/structure alignments, and homology modeling within PyMOL.
GEne Cluster prediction with COnditional random fields.
Visualise RNA secondary structure in consistent, reproducible and recognisable layouts
OhmNet: Representation learning in multi-layer graphs
Genome size estimation from long read overlaps
A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category
Identification of errors in draft genome assemblies with single-base pair resolution for quality assessment and improvement
a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies
LAMBDA – the Local Aligner for Massive Biological DatA
🫧🧬 From fragmented assemblies to high-quality bacteriophage genomes
Scripts, utilities and programs for genomic bioinformatics.
tiara – a tool for DNA sequence classification
A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data
:card_index: Retrieve data in genomic intervals with a Python interface for tabix.
A Julia package to analyze protein sequences, structures, and evolutionary information
:construction_worker: Fasten toolkit, for streaming operations on fastq files
FlashFry: The rapid CRISPR target site characterization tool
Snakemake-based workflow for detecting structural variants in genomic data
Algorithm For Gene Order Reconstruction in Ancestors
🧬 ManyFold: An efficient and flexible library for training and validating protein folding models
Lynn Langit profile
🍪 SEnsible Step-wise Analysis of DNA MEthylation BeadChips
ChIP-Atlas: Browse and analyze all public ChIP/DNase-seq data on your browser
Fast and flexible ORF finder
A C library for handling bigWig files
A course on genomics and bioinformatics from WashU