Most popular bioinformatics repositories and open source projects

bamtocov

🏔 coverage extraction from BAM/CRAM files, supporting targets 📊  

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DeepInteract

A geometric deep learning pipeline for predicting protein interface co...

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AGFusion

Python package to annotate and visualize gene fusions.

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scMerge

Statistical approach for removing unwanted variation from multiple sin...

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LRSIM

10x Genomics Reads Simulator

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newt

A web application to visualize and edit pathway models

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hts-nim-tools

useful command-line tools written to showcase hts-nim

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specs

BioContainers specifications

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RDPTools

Collection of commonly used RDP Tools for easy building

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CHM-eval

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iva

de novo virus assembler of Illumina paired reads

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fasten

:construction_worker: Fasten toolkit, for streaming operations on fast...

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Biochat

Natural language processing of Gene Expression Omnibus data

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BioD

A D library for computational biology and bioinformatics

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sample-sheet

A permissively licensed library designed to replace Illumina's Experim...

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cromshell

CLI for interacting with Cromwell servers

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GOSemSim

:golf: GO-terms Semantic Similarity Measures

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tutorials

:books: Various bioinformatics tutorials

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R2DT

Visualise RNA secondary structure in consistent, reproducible and reco...

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BioMedical-NLP-corpus

Biomedical NLP Corpus or Datasets.

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Finder

A fully automated gene annotator from RNA-Seq expression data

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deepsignal-plant

Detecting methylation using signal-level features from Nanopore sequen...

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MungeSumstats

Rapid standardisation and quality control of GWAS or QTL summary stati...

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sequence_align

Efficient implementations of Needleman-Wunsch and other sequence align...

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covid19-event-risk-planner

COVID19 risk planner R-Shiny application

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ensembl-compara

The Ensembl Compara Perl API and SQL schema

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migmap

HTS-compatible wrapper for IgBlast V-(D)-J mapping tool

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BioKEEN

A computational library for learning and evaluating biological knowled...

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bin

My bioinfo toolbox

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sirius-libs

sirius-libs - Metabolomics mass spectrometry framework for molecular f...

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protr

Comprehensive toolkit for generating various numerical features of pro...

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HTStream

A high throughput sequence read toolset using a streaming approach fa...

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maui

Multi-omics Autoencoder Integration: Deep learning-based heterogenous...

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covid19kg

COVID-19 Knowledge Graph: a computable, multi-modal, cause-and-effect...

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Contextualized

A statistical machine learning toolbox for estimating models, distribu...

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awesome-structural-bioinformatics

Structural Bioinformatics is awesome. Throw your textbook in the garba...

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imcs21-cblue

This is the repo of the medical dialogue dataset 'imcs21' in CBLUE@Tia...

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bistro

A library to build and execute typed scientific workflows

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sevenbridges-python

SevenBridges Python Api bindings

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coge

CoGe (Comparative Genomics) Platform

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ginkgo

Cloud-based single-cell copy-number variation analysis tool

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mitre

The Microbiome Interpretable Temporal Rule Engine

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Bioinformatics

Bioinformatics analysis scripts, workflows, general code examples

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DeepRTplus

Deep (Transfer) Learning for Peptide Retention Time Prediction

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HiC_pipeline

An easy-to-use Hi-C data processing software supporting distributed co...

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Integron_Finder

Bioinformatics tool to find integrons in bacterial genomes

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dentist

Close assembly gaps using long-reads at high accuracy.

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ggcat

Compacted and colored de Bruijn graph construction and querying

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chembl-downloader

Write reproducible code for getting and processing ChEMBL

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rkmh

Classify sequencing reads using MinHash.

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