Search Results for "genomics"
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Showing 131 open source projects for "genomics"
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Seurat
R toolkit for single cell genomics
Seurat is a comprehensive R toolkit for single-cell genomics analysis, introduced by the Satija Lab at NYGC. It supports quality control, normalization, clustering, integration of multimodal data (e.g., scRNA‑seq, spatial, CITE‑seq), and visualization. Seurat v5 introduces scalable workflows and spatial transcriptomics support, commonly used in academic and industry research for single-cell studies. -
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Volcano
A Cloud Native Batch System (Project under CNCF)
...It provides a suite of mechanisms that are commonly required by many classes of batch & elastic workload including machine learning/deep learning, bioinformatics/genomics, and other "big data" applications. These types of applications typically run on generalized domain frameworks like TensorFlow, Spark, Ray, PyTorch, MPI, etc, which Volcano integrates with. Volcano builds upon a decade and a half of experience running a wide variety of high-performance workloads at scale using several systems and platforms, combined with best-of-breed ideas and practices from the open-source community. ... -
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vcf2maf
Convert a VCF into a MAF
vcf2maf is a Perl-based tool developed by the Memorial Sloan Kettering Cancer Center to convert Variant Call Format (VCF) files into Mutation Annotation Format (MAF) files. This conversion standardizes variant annotations, facilitating downstream analyses in cancer genomics. -
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Claude Scientific Skills
A set of ready to use Agent Skills for research, science, engineering
Claude Scientific Skills is a large open source collection of ready-to-use scientific capabilities that extend AI coding agents into full research assistants. The project provides more than 170 curated skills covering domains such as genomics, drug discovery, medical imaging, physics, and advanced data analysis. Each skill bundles documentation, examples, and tool integrations so agents can reliably execute complex multi-step scientific workflows. The framework follows the open Agent Skills standard and works with multiple AI development environments including Claude Code, Cursor, and Codex. ... -
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Prokka
Rapid prokaryotic genome annotation
...The pipeline is optimized for speed, using multithreading and caching to annotate large microbial genomes in minutes. Because it standardizes names, locus tags, and qualifiers, Prokka is often used as a baseline for comparative microbial genomics, pangenome studies, and functional profiling. Its modular design lets users plug in custom gene callers or databases, making it flexible for diverse research contexts. -
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MedgeClaw
Open-source AI research assistant for biomedicine
MedgeClaw is a specialized AI-powered research assistant tailored for biomedical and scientific workflows, built on top of OpenClaw and Claude Code architectures. It integrates a large library of domain-specific skills, enabling it to perform complex analyses in areas such as genomics, drug discovery, and clinical research. The system connects conversational interfaces with computational environments, allowing users to initiate research tasks through messaging platforms while the backend executes analyses using tools like R and Python. It includes a real-time dashboard that displays progress, generated code, and outputs, providing transparency throughout the research process. ... -
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AWS ParallelCluster Cookbook
The Chef cookbook used to build and bootstrap AWS ParallelCluster
...It automatically sets up the required compute resources and a shared filesystem and offers a variety of batch schedulers such as AWS Batch and Slurm. AWS ParallelCluster facilitates both quick start proof of concepts (POCs) and production deployments. You can build higher-level workflows, such as a Genomics portal that automates the entire DNA sequencing workflow, on top of AWS ParallelCluster. Node.js is required by AWS CDK library used by ParallelCluster. -
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AWS ParallelCluster Node
Python package installed on the Amazon EC2 instances
...It automatically sets up the required compute resources and a shared filesystem and offers a variety of batch schedulers such as AWS Batch and Slurm. AWS ParallelCluster facilitates both quick start proof of concepts (POCs) and production deployments. You can build higher-level workflows, such as a Genomics portal that automates the entire DNA sequencing workflow, on top of AWS ParallelCluster. -
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GenoViz
Visualization software for genomics
GenoViz provides software applications and re-usable components for data visualization and data sharing in genomics. Our main products are * Integrated Genome Browser (IGB) * GenoViz SDK For more information about IGB, visit https://bioviz.org. Source code for IGB is available from https://bitbucket.org/lorainelab/integrated-genome-browser. For more information about GenoViz SDK, visit https://bitbucket.org/lorainelab/genoviz-sdk. -
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popoolation
estimate natural variation and positive selection
...Currently PoPoolation allows to calculate Tajima’s Pi, Watterson’s Theta and Tajima’s D with a sliding window approach for chromosomes or for set of genes. One of the main challenges in population genomics is to identify regions of intererest on a genome wide scale. We believe that PoPoolation will greatly aid this task by allowing a fast and user friendly analysis of NGS data from DNA pools. Documentation: https://sourceforge.net/p/popoolation/wiki/Main/ -
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GeneMiner2 is a comprehensive toolkit designed for phylogenomic genomics. Its main functionalities include: - Mining single-copy nuclear genes, plastid genes/genomes, and other molecular markers from next-generation sequencing data. - Aligning and trimming multiple molecular markers, constructing concatenated and coalescent-based phylogenetic trees, and calibrating tree time. Reference for GeneMiner2: Yu XY, Tang ZZ, Zhang Z, Song YX, He H, Shi Y, Hou JQ, Yu Y. 2026.
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...Please cite the BRIG paper if BRIG is used to generate figures for publications: NF Alikhan, NK Petty, NL Ben Zakour, SA Beatson (2011) BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons, BMC Genomics, 12:402. PMID: 21824423
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PLEK
predictor of long non-coding RNAs and mRNAs based on k-mer scheme
....: https://doi.org/10.1186/s12864-024-10662-y Aimin Li, Haotian Zhou, Siqi Xiong, et al. PLEKv2: predicting lncRNAs and mRNAs based on intrinsic sequence features and the coding-net model. BMC Genomics 2024, 25(1):756. -
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PLEKv2
PLEKv2: predicting lncRNAs and mRNAs
...decompress Coding_Net_kmer6_orf_Arabidopsis.h5.bz2 model $ bunzip2 Coding_Net_kmer6_orf_Arabidopsis.h5.bz2 USAGE Python PLEK2.py -i fasta_file -m model(ve: vertebrate , pl: plant) Examples: $ python PLEK2.py -i test.fasta -m ve Aimin Li, Haotian Zhou, Siqi Xiong, Junhuai Li, Saurav Mallik, Rong Fei, Yajun Liu, Hongfang Zhou, Xiaofan Wang, Xinhong Hei, Lei Wang. PLEKv2: predicting lncRNAs and mRNAs based on intrinsic sequence features and the coding-net model. BMC Genomics 2024, 25(1):756. https://doi.org/10.1186/s12864-024-10662-y -
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Gemi
PCR primers / probes design from multiple & degenerate sequences
...Gemi can parse large dataset of sequences efficiently. Python codes can be supported upon request. Article: Gemi: PCR primers prediction from multiple alignments Comparative and functional genomics 2012;2012:783138 DOI: https://doi.org/10.1155/2012/783138 PMID: https://www.ncbi.nlm.nih.gov/pubmed/23316117 PMCID: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3535827/ -
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OmicsSuite
OmicsSuite: a suite for multi-omics analysis and visualization.
OmicsSuite (https://github.com/OmicsSuite/, https://omicssuite.github.io), original name BioSciTools, a desktop program developed based on Java 11, aims to make new exploration and contribution to the development of bioinformatics, and realize data analysis and visualization in the fields of sequence analysis, multimomics (transcriptomics, genomics, protein omics, metabonomics, single cell), microbiology, clinical, etc. The program inherits the excellent interactive components, perfect analysis function and beautiful operation interface of HiPlot (https://hiplot.cn), which I developed based VUE.js and Node.js, etc. -
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...The methods implemented in Shetti are simple and basic commands with friendly user interface. Article: Haitham Sobhy; Shetti, a simple tool to parse, manipulate and search large datasets of sequences; Microbial Genomics; 2015; doi: 10.1099/mgen.0.000035; PMID: 28348820
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....; Malyutina, A.; Shadbahr, T.; Tanoli Z; Pessia, A.; Tang, J. SynergyFinder Plus: Toward Better Interpretation and Annotation of Drug Combination Screening Datasets. Genomics, Proteomics & Bioinformatics 2022, 20, 587-596 https://doi.org/10.1016/j.gpb.2022.01.004
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scArches
Reference mapping for single-cell genomics
Single-cell architecture surgery (scArches) is a package for reference-based analysis of single-cell data. scArches allows your single-cell query data to be analyzed by integrating it into a reference atlas. By mapping your data into an integrated reference you can transfer cell-type annotation from reference to query, identify disease states by mapping to healthy atlas, and advanced applications such as imputing missing data modalities or spatial locations. -
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DeepMind Research
Implementations and code to accompany DeepMind publications
...The top level organizes many paper-specific directories across domains such as deep reinforcement learning, self-supervised vision, generative modeling, scientific ML, and program synthesis—for example BYOL, Perceiver/Perceiver IO, Enformer for genomics, MeshGraphNets for physics, RL Unplugged, Nowcasting for weather, and more. Each project folder typically includes its own README, scripts, and notebooks so you can run experiments or explore models in isolation, and many link to associated datasets or external environments like DeepMind Lab and StarCraft II. The codebase is primarily Jupyter Notebooks and Python, reflecting an emphasis on experimentation and pedagogy rather than production packaging. -
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Amazon Genomics CLI
Tool to simplify the processes of deploying the AWS infrastructure
Amazon Genomics CLI is an open-source CLI that helps customers run genomics workflows in the cloud by automating the deployment of best practices infrastructure for workflow engines. Amazon Genomics CLI reduces the time for scientists and developers to start running existing genomics workflows at scale and speeds up iteration cycles as they develop new ones. -
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CodonU
A python project for analysis of codon usage for gene or genome analys
...This open-source project incorporates various statistical measures necessary for codon usage analysis, including codon adaptation index, codon bias index, Gravy score, and correspondence analysis for both nucleotide and protein sequences. Start using CodonU today and see how it can revolutionize your genomics research! Find more at: https://github.com/SouradiptoC/CodonU Documentation link: https://souradiptoc.github.io/CodonU Example Link: https://github.com/SouradiptoC/CodonU/tree/master/Examples -
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Data Analysis for the Life Sciences
Rmd source files for the HarvardX series PH525x
...It is part of a larger ecosystem: the compiled HTML / book version of the labs is published via a companion “book” repository, which presents a polished, browsable version of the materials. The content covers topics such as data wrangling in R, statistical inference, genomics workflows, Bioconductor packages, and project-based analyses. Because it’s open and modular, contributors can suggest improvements, update modules, or add new exercises. -
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misc genomics tools
Various scripts used in sequencing, annotation and RNAseq analysis
This is a collection of various programs developed in the course of a genomics project, involving the Pseudomonas strain NCIMB10586 These include * identifying and correcting errors in an (eg) pacbio genome sequence using illumina reads * prokaryotic sequence/genome annotation * RNAseq analysis - normalisation and collation of multiple samples as a group * RNAseq visualisation All scripts are provided on a 'best efforts' basis, however due to various system changes I do not guarantee that all files are the version used in the analysis. ... -
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vipie
http://vipie.rd.tuni.fi/vipie/index.html
Open access and web based virome population profiling for multi-sample metagenomics NGS, please note that the web server has been updated to: http://vipie.rd.tuni.fi/vipie/index.html Now supporting COVID-19 User guide: http://vipie.rd.tuni.fi/vipie/doc/vipie_user_guide.pdf Open access: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3721-7 Please cite: Lin, J., Kramna, L., Autio, R. et al. Vipie: web pipeline for parallel characterization of viral populations from multiple NGS samples. BMC Genomics 18, 378 (2017). https://doi.org/10.1186/s12864-017-3721-7
