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2,716 search results found

Cs Video Courses ⭐ 62,887

List of Computer Science courses with video lectures.

Dash ⭐ 19,976

Data Apps & Dashboards for Python. No JavaScript Required.

Biopython ⭐ 3,918

Official git repository for Biopython (originally converted from CVS)

Deepvariant ⭐ 2,978

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

Awesome Single Cell ⭐ 2,784

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

Awesome Bioinformatics ⭐ 2,505

A curated list of awesome Bioinformatics libraries and software.

Nextflow ⭐ 2,447

A DSL for data-driven computational pipelines

Scanpy ⭐ 1,753

Single-cell analysis in Python. Scales to >1M cells.

Oneliners ⭐ 1,705

Useful bash one-liners for bioinformatics.

Minimap2 ⭐ 1,613

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Fastp ⭐ 1,602

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging.

Official code repository for GATK versions 4 and up

Scispacy ⭐ 1,548

A full spaCy pipeline and models for scientific/biomedical documents.

Bioconda Recipes ⭐ 1,539

Conda recipes for the bioconda channel.

Awesome Deepbio ⭐ 1,467

A curated list of awesome deep learning applications in the field of computational biology

Rust Bio ⭐ 1,428

This library provides implementations of many algorithms and data structures that are useful for bioinformatics. All provided implementations are rigorously tested via continuous integration.

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

Mmseqs2 ⭐ 1,235

MMseqs2: ultra fast and sensitive search and clustering suite

Galaxy ⭐ 1,211

Data intensive science for everyone.

Multiqc ⭐ 1,159

Aggregate results from bioinformatics analyses across many samples into a single report.

Seqtk ⭐ 1,148

Toolkit for processing sequences in FASTA/Q formats

Seqkit ⭐ 1,133

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation

Scipipe ⭐ 1,010

Robust, flexible and resource-efficient pipelines using Go and the commandline

Getting Started With Genomics Tools And Resources ⭐ 991

Unix, R and python tools for genomics and data science

ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.

A language and runtime for distributed, incremental data processing in the cloud

Cromwell ⭐ 944

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

Deep_gcns_torch ⭐ 940

Pytorch Repo for DeepGCNs (ICCV'2019 Oral, TPAMI'2021), DeeperGCN (arXiv'2020) and GNN1000(ICML'2021): https://www.deepgcns.org

Graphein ⭐ 932

Protein Graph Library

A cross-platform, efficient and practical CSV/TSV toolkit in Golang

Cloud-native genomic dataframes and batch computing

Therapeutics Data Commons: Artificial Intelligence Foundation for Therapeutic Science

React Plotly.js ⭐ 884

A plotly.js React component from Plotly 📈

Scikit Bio ⭐ 833

scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.

Deeppurpose ⭐ 826

A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)

Ncbi Genome Download ⭐ 784

Scripts to download genomes from the NCBI FTP servers

A cross-platform command-line tool for executing jobs in parallel

C library for high-throughput sequencing data formats

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

Workflow Description Language - Specification and Implementations

Nucleus ⭐ 675

Python and C++ code for reading and writing genomics data.

Biopandas ⭐ 673

Working with molecular structures in pandas DataFrames

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

Python library to facilitate genome assembly, annotation, and comparative genomics

Bwa Mem2 ⭐ 645

The next version of bwa-mem

Deeptools ⭐ 644

Tools to process and analyze deep sequencing data.

A high-performance, Pythonic language for bioinformatics

Containers ⭐ 621

Bioinformatics containers

A Go package for engineering organisms.

Vsearch ⭐ 605

Versatile open-source tool for microbiome analysis

Bowtie2 ⭐ 594

A fast and sensitive gapped read aligner

Plantcv ⭐ 590

Plant phenotyping with image analysis

Incubator for useful bioinformatics code, primarily in Python and R

Awesome ⭐ 565

Awesome resources on Bioinformatics, data science, machine learning, programming language (Python, Golang, R, Perl) and miscellaneous stuff.

Biojava ⭐ 564

📖🔬☕ BioJava is an open-source project dedicated to providing a Java library for processing biological data.

Biostar Central ⭐ 563

Dgl Lifesci ⭐ 558

Python package for graph neural networks in chemistry and biology

Dash Cytoscape ⭐ 555

Interactive network visualization in Python and Dash, powered by Cytoscape.js

Sambamba ⭐ 552

Tools for working with SAM/BAM data

Foldseek ⭐ 545

Foldseek enables fast and sensitive comparisons of large structure sets.

A scikit-learn compatible library for graph kernels

BWK awk modified for biological data

Biotite ⭐ 515

A comprehensive library for computational molecular biology

Dnafeaturesviewer ⭐ 500

👁️ Python library to plot DNA sequence features (e.g. from Genbank files)

Nanopolish ⭐ 496

Signal-level algorithms for MinION data

Anndata ⭐ 495

Annotated data.

Dash Bio ⭐ 485

Open-source bioinformatics components for Dash

Sniffles ⭐ 479

Structural variation caller using third generation sequencing

Pycirclize ⭐ 476

Circular visualization in Python (Circos Plot, Chord Diagram)

Dash.jl ⭐ 475

Dash for Julia - A Julia interface to the Dash ecosystem for creating analytic web applications in Julia. No JavaScript required.

Cutadapt ⭐ 475

Cutadapt removes adapter sequences from sequencing reads

Awesome Cheminformatics ⭐ 473

A curated list of Cheminformatics libraries and software.

Pydeseq2 ⭐ 470

A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

Yet another redundant workflow engine

Circosjs ⭐ 454

d3 library to build circular graphs

The Chemistry Development Kit

Clinker ⭐ 452

Gene cluster comparison figure generator

Hifiasm ⭐ 443

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Megahit ⭐ 442

Ultra-fast and memory-efficient (meta-)genome assembler

Jvarkit ⭐ 440

Java utilities for Bioinformatics

Jbrowse ⭐ 437

Full-featured and stable genome browser built with JavaScript and HTML5.

Simple Gpu ⭐ 432

🦒 Functional WebGPU

Sourmash ⭐ 431

Quickly search, compare, and analyze genomic and metagenomic data sets.

Biocode ⭐ 430

Bioinformatics code libraries and scripts

Hh Suite ⭐ 429

Remote protein homology detection suite.

Accurate sample inference from amplicon data with single nucleotide resolution

Pyfaidx ⭐ 427

Efficient pythonic random access to fasta subsequences

Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.

Cobrapy ⭐ 414

COBRApy is a package for constraint-based modeling of metabolic networks.

✂️ ⚡ Rapid haploid variant calling and core genome alignment

React Cytoscapejs ⭐ 407

React component for Cytoscape.js network visualisations

Maftools ⭐ 400

Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.

An analysis and visualization platform for 'omics data

Noodles ⭐ 384

Bioinformatics I/O libraries in Rust

GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.

Bioruby ⭐ 369

Deep_learning_examples ⭐ 367

Examples of using deep learning in Bioinformatics

Single Cell Pseudotime ⭐ 367

An overview of algorithms for estimating pseudotime in single-cell RNA-seq data

Minigraph ⭐ 367

Proof-of-concept seq-to-graph mapper and graph generator

Related Searches

Python Bioinformatics (1,701)

Bioinformatics Genomics (541)

R Bioinformatics (490)

Bioinformatics Genome (445)

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