bioinformatics
Repositories (1466)
Identification of errors in draft genome assemblies with single-base pair resolution for quality assessment and improvement
just annotate it, dammit!
Robust and efficient workflows using a simple language agnostic approach
Spatial-Linked Alignment Tool
Tools for manipulating annotated data matrices
AI-powered IDE for bioinformatics — built by biologists, for biologists
Prediction of key transcription factors in cell fate determination using enhancer networks. See full ANANSE documentation for detailed installation in...
Portable command-line tool to query bioinformatics APIs, data, databases and files.
Write reproducible code for getting and processing ChEMBL
Inference of microbial interaction networks from large-scale heterogeneous abundance data
Genome size estimation from long read overlaps
ClairS-TO - a deep-learning method for tumor-only somatic variant calling
Bioinformatics tool to find integrons in bacterial genomes
Collection of cloud-based biomedical data science learning modules funded by the National Institute of General Medical Sciences at the NIH
1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates
Deep Learning based cell composition analysis with Scaden.
Race and ethnicity Imputation from Disease history with Deep LEarning
[Bioinformatics 2021] This is the repo for the paper `SumGNN: Multi-typed Drug Interaction Prediction via Efficient Knowledge Graph Summarization'.
a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference
Blender plugin to process biological data and molecular work.
Universal and efficient structure-based core gene phylogeny with Foldseek and ProstT5
An aviary-based data science agent based on jupyter notebooks
Massively parallel phylogenetic placement of genetic sequences
Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).
Provide R access to the NCI Genomic Data Commons portal.
TypeDB Bio: Biomedical Knowledge Graph
Infectious Disease Sequencing Platform
SIB course on single cell transcriptomics by mostly using the Seurat pipeline
Intuitive guide to multi-omics integration with toy examples: supervised latent components (DIABLO), unsupervised shared/partial/unique structure (DIV...
Calculation of interatomic interactions in molecular structures
A collection of reusable WDL tasks. Category:Other
RNA modifications detection from Nanopore dRNA-Seq data
a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies
biotoolsregistry: discovery portal for bioinformatics software and databases
DeepSpot: Deep learning model for predicting spatial transcriptomics from H&E histopathology images. Supports spot-level (Visium) and single-cell (Xen...
GO enrichment with python -- pandas meets networkx
List of tools and resources related to the 10x Genomics GEMCode/Chromium system
The START App: R Shiny Transcriptome Analysis Resource Tool
vcfdist: Accurately benchmarking phased variant calls
Yet Another Chimeric Read Detector
tiara – a tool for DNA sequence classification
:dart: Human transcription factor target genes from 6 databases in convenient R format.
A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment
A course on genomics and bioinformatics from WashU
PyMod 3 - sequence similarity searches, multiple sequence/structure alignments, and homology modeling within PyMOL.
Algorithm For Gene Order Reconstruction in Ancestors
Python package and CLI for whole-genome duplication related analyses. **This package is deprecated in favor of** https://github.com/heche-psb/wgd.
Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.
BANKSY: Spatial Clustering Algorithm that Unifies Cell-Typing and Tissue Domain Segmentation. Python package for spatial transcriptomics analysis.
GEne Cluster prediction with COnditional random fields.