bioinformatics

List of Computer Science courses with video lectures.

Data Apps & Dashboards for Python. No JavaScript Required.

Official git repository for Biopython (originally converted from CVS)

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

A curated list of awesome Bioinformatics libraries and software.

A DSL for data-driven computational pipelines

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

Single-cell analysis in Python. Scales to >100M cells.

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

Conda recipes for the bioconda channel.

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Official code repository for GATK versions 4 and up

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

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

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

Toolkit for processing sequences in FASTA/Q formats

Data intensive science for everyone.

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

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

Therapeutics Commons (TDC-2): Multimodal Foundation for Therapeutic Science

A plotly.js React component from Plotly 📈

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

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

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

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

MMseqs2: ultra fast and sensitive search and clustering suite

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

Unix, R and python tools for genomics and data science

Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)

A comprehensive tutorial about GWAS and PRS

Cloud-native genomic dataframes and batch computing

Protein Graph Library

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

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

Scripts to download genomes from the NCBI FTP servers

A curated list of Cheminformatics libraries and software.

Bioinformatics containers

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

A high-performance, Pythonic language for bioinformatics

C library for high-throughput sequencing data formats

Workflow Description Language - Specification and Implementations

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

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

Working with molecular structures in pandas DataFrames

The next version of bwa-mem

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

Gene cluster comparison figure generator

Python package for graph neural networks in chemistry and biology

Tools to process and analyze deep sequencing data.

Versatile open-source tool for microbiome analysis