70 Open source projects that are alternatives of or similar to cosmosR

BACNET is a Java based platform to develop website for multi-omics analysis

Translator of spreadsheet mappings into R2RML, RML or YARRRML

Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm

A Quality Control (QC) pipeline for Proteomics (PTX) results generated by MaxQuant

Quantitative features for mass spectrometry data

A Python framework for integrating biological databases and structured data sources in Biological Expression Language (BEL)

📚 🔬 PIA - Protein Inference Algorithms

Reference mapping for single-cell genomics

Highly adaptable common interface for proteomics search and de novo engines

An ontology of cell types

Digital Cell Sorter (DCS): single cell RNA-seq analysis toolkit. Documentation:

Using R and Bioconductor packages for the analysis and comprehension of proteomics data.

Population Assignment using Genetic, Non-genetic or Integrated Data in a Machine-learning Framework. Methods in Ecology and Evolution. 2018;9:439–446.

pyQms, generalized, fast and accurate mass spectrometry data quantification

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

PyProphet: Semi-supervised learning and scoring of OpenSWATH results.

📖 Generation and Applications of Knowledge Graphs in Systems and Networks Biology

Fast and flexible semi-supervised learning for peptide detection in Python

Some of the projects i made when starting to learn R for Data Science at the university

Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)

Template to deploy a Data Product for data stream processing into a Data Landing Zone of the Data Management & Analytics Scenario (former Enterprise-Scale Analytics). The Data Product template can be used by cross-functional teams to ingest, provide and create new data assets within the platform.

🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.

Installer for Thymeflow, a personal knowledge management system.

Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics

A prediction model for differential gene expression (DE) based on genome-wide regulatory interactions

Code pipeline for the PaccMann^RL in iScience: https://www.cell.com/iscience/fulltext/S2589-0042(21)00237-6

Feature Annotation Location Description Ontology

Configurable data bridge for permanent ETL jobs

Open source Java library for computational proteomics

Upserts, Deletes And Incremental Processing on Big Data.

A Comet-based, best practices proteomics pipeline.

A .NET class library that allows you to import data from different sources into a unified destination

No description or website provided.

Framework and command-line tools for integrating FollowTheMoney data streams from multiple sources

The repo for LFQ-Analyst

Building data processing pipelines for documents processing with NLP using Apache NiFi and related services

Interpretation of proteomics identification results

A lightweight opinionated ETL framework, halfway between plain scripts and Apache Airflow

pDeep: Predicting MS/MS Spectra of Peptides with Deep Learning

Powerful RDF Knowledge Graph Generation with [R2]RML Mappings

The Proteomics Experimental Design file format: Standard for experimental design annotation

🧪 🖥 Transparent exploration of machine learning for biomarker discovery from proteomics and omics data

A complete toolkit for shotgun proteomics data analysis

A bioinformatics API and web-app to integrate multi-omics datasets & interface with public databases.

Method for Identifying Novel Transcripts and Isoforms using Equivalence classes, in cancer and rare disease.

Template to deploy a Data Product for Batch data processing into a Data Landing Zone of the Data Management & Analytics Scenario (former Enterprise-Scale Analytics). The Data Product template can be used by cross-functional teams to ingest, provide and create new data assets within the platform.

Expression Weighted Celltype Enrichment. See the package website for up-to-date instructions on usage.

WInte.r is a Java framework for end-to-end data integration. The WInte.r framework implements well-known methods for data pre-processing, schema matching, identity resolution, data fusion, and result evaluation.

MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets

Privacy and Security focused Segment-alternative, in Golang and React

Reference-based transcript discovery from long RNA read

Multiome GRN inference.

just annotate it, dammit!

Kuwala is the no-code data platform for BI analysts and engineers enabling you to build powerful analytics workflows. We are set out to bring state-of-the-art data engineering tools you love, such as Airbyte, dbt, or Great Expectations together in one intuitive interface built with React Flow. In addition we provide third-party data into data sc…

Compare different differential abundance and expression methods

The Common Core Ontology Repository holds the current released version of the Common Core Ontology suite.

Workshop on tidytranscriptomics: Performing tidy transcriptomics analyses with tidybulk, tidyverse and tidyheatmap

Airbyte is an open-source EL(T) platform that helps you replicate your data in your warehouses, lakes and databases.

An Efficient RML-Compliant Engine for Knowledge Graph Construction

Prize-Collecting Steiner Forests for Interactomes