bioinformatics

protein structure generation with sparse all-atom denoising models

Various utilities regarding Levenshtein transducers. (Java)

Protein Alignment and Detection Interface

A web application to visualize and edit pathway models

Useful bioinformatic scripts

Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).

Reference-free reconstruction and error correction of transcriptomes from Nanopore long-read sequencing

Estimate metagenomic coverage and sequence diversity

Graph neural network for generating novel amino acid sequences that fold into proteins with predetermined topologies.

Remove contaminated contigs from genomes using k-mers and taxonomies.

Benchmark datasets for WGS analysis of SARS-CoV-2. (https://peerj.com/articles/13821/)

dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify Transposable E...

⚡️ 🧬 Fulgor is a fast and space-efficient colored de Bruijn graph index.

Generating biologically informed neural networks

Single-cell spatial omics analysis that makes you happy!

Support Vector Structural Variation Genotyper

Pattern Recognition for Cell-free DNA

Lightweight Iterative Gene set Enrichment in R

release version

Variant Calling Pipeline Using GATK4 and Nextflow

Interactive Python notebooks for PDBe API training

A Snakemake workflow and MrBiomics module for processing and visualizing (multimodal) sc/snRNA-seq data generated with 10X Genomics Kits or in the MTX...

Benchmarking different languages for a simple bioinformatics task (Counting the GC fraction of DNA in a FASTA file)

A Python platform for Structural Bioinformatics

de novo virus assembler of Illumina paired reads

An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads.

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

Frequently used commands in bioinformatics

circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data

Beyondcell is a computational methodology for identifying tumour cell subpopulations with distinct drug responses in single-cell RNA-seq and Spatial T...

quickly filter fastq files by matching sequences to a set of regex patterns

A minimal desktop app for easy and convenient gene annotation and lookup.

Improve the quality of a denovo assembly by scaffolding and gap filling

sirius-libs - Metabolomics mass spectrometry framework for molecular formula identification of small molecules written in Java

Cloud engine and platform for metabolite annotation for imaging mass spectrometry

Awesome list for all things AI, ML and deep learning

Colocalization analysis of genetic association signals

GTDB taxonomy taxdump files with trackable TaxIds

A Snakemake workflow and MrBiomics module for easy visualization of genome browser tracks of aligned BAM files (e.g., RNA-seq, ATAC-seq, scRNA-seq, .....

A fast tool for detecting and decomposing segmental duplications in genome assemblies

A curated list of awesome self-learning materials in Computational Structural Biology, such as sources, tutorials, etc.

DICOM parser for golang

Bioinformatics analysis scripts, workflows, general code examples

VAPiD: Viral Annotation and Identification Pipeline

List of IARC bioinformatics pipelines and resources

A Snakemake workflow and MrBiomics module for performing perturbation analyses of pooled (multimodal) CRISPR screens with sc/snRNA-seq read-out (scCRI...

A Snakemake workflow and MrBiomics module for performing differential expression analyses (DEA) on (multimodal) sc/snRNA-seq data powered by the R pac...

Comprehensive Python client for the Uniprot REST API

NeuroGNN is a state-of-the-art framework for precise seizure detection and classification from EEG data. It employs dynamic Graph Neural Networks (GNN...

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