bioinformatics

Detection of remote homology by comparison of protein language model representations

Code for design of diagnostic PCR primers, and metabarcoding markers.

A package to annotate protein sequences

Biomedical NLP Corpus or Datasets.

PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.

生物信息学项目实践仓库🏆🥇

Minimum Information about any (X) Sequence” (MIxS) specification

protein structure generation with sparse all-atom denoising models

A web application to visualize and edit pathway models

PathwayMapper: An interactive and collaborative graphical curation tool for cancer pathways

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

Estimate metagenomic coverage and sequence diversity

:books: Various bioinformatics tutorials

A fully automated gene annotator from RNA-Seq expression data

Allele-specific alignment sorting

Deep learning-based tissue compositions and cell-type-specific gene expression analysis with tissue-adaptive autoencoder (TAPE)

A high-performance modification detection tool in Rust

Rust crates for working with Workflow Description Language (WDL) documents.

Fast and accurate label-free quantification for small and very large numbers of proteomes

Generating biologically informed neural networks

Interactive Python notebooks for PDBe API training

Protein Alignment and Detection Interface

Docker for 4DN Hi-C processing pipeline

slurmR: A Lightweight Wrapper for Slurm

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

GA4GH Variation Representation Python Implementation

Bioinformatics on GCP, AWS or Azure

release version

Reference-based consensus creation

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

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

GTDB taxonomy taxdump files with trackable TaxIds

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

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

Various utilities regarding Levenshtein transducers. (Java)

Useful bioinformatic scripts

Colocalization analysis of genetic association signals

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

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

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

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

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

Support Vector Structural Variation Genotyper

Pattern Recognition for Cell-free DNA

Lightweight Iterative Gene set Enrichment in R

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

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

Frequently used commands in bioinformatics

Variant Calling Pipeline Using GATK4 and Nextflow