79 Open source projects that are alternatives of or similar to RforProteomics

Quantitative features for mass spectrometry data

Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics

A complete toolkit for shotgun proteomics data analysis

The repo for LFQ-Analyst

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

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

This is the git repository matching the Bioconductor package xcms: LC/MS and GC/MS Data Analysis

No description or website provided.

pyQms, generalized, fast and accurate mass spectrometry data quantification

This is the ensembldb development repository.

Library for mass spectrometry projects

📚 🔬 PIA - Protein Inference Algorithms

The pmartR R package provides functionality for quality control, normalization, exploratory data analysis, and statistical analysis of mass spectrometry (MS) omics data, in particular proteomic (either at the peptide or the protein level), lipidomic, and metabolomic data. This includes data transformation, specification of groups that are to be …

Bioconductor package for management of multi-assay data

Thermo MSFileReader Python bindings

Interactive Differential Expression AnaLysis - DE made accessible and reproducible

Haskell library containing isotopic masses and relative abundances for elements from Hydrogen to Bismuth and Thorium and Uranium (excluding Technetium and promethium), i.e., all elements with naturally-occurring isotopes.

Modeling and correcting fragment sequence bias for RNA-seq

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

Glycan Analysis and Glycoinformatics Library for Python

A MALDI Mass Spectrometry Bioinformatics Platform

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

Mass spectrometry data visualization

Open source Java library for computational proteomics

Create a cromphensive report of DEG list coming from any analysis of RNAseq data

Organic/biological mass spectrometry data analysis (development version).

A library for deisotoping and charge state deconvolution of complex mass spectra

Public Workflows at GNPS

Interactive R package to quantify, analyse and visualise alternative splicing

📚 RDocumentation provides an easy way to search the documentation for every version of every R package on CRAN and Bioconductor.

Enjoy your transcriptomic data and analysis responsibly - like sipping a cocktail

A R framework for pipeline benchmarking, with application to single-cell RNAseq

Contribute Packages to Bioconductor

Elastic, reproducible, and reusable genomic data science tools from R backed by cloud resources

Quantum mechanic mass spectrometry calculation program

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

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

Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles

AnaLysis routines for ePigenomicS data - 🏫 Bioconductor project

Fast and Accurate CE-, GC- and LC-MS(/MS) Data Processing

COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.

Stickers for some Bioconductor packages - feel free to contribute and/or modify.

.NET DLL wrapper for reading Thermo .Raw files. Uses ThermoFisher.CommonCore NuGet packages provided by Thermo Fisher Scientific

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

Convert between AnnData and SingleCellExperiment

Reproducible reanalysis of a combined ChIP-Seq & RNA-Seq data set

📚 R interface to the Bio-Formats library

Brings Orbitrap Mass Spectrometry Data to Life; Multi-platform, Fast and Colorful R package.

Materials on the analysis of microarray expression data; focus on re-analysis of public data ( http://tinyurl.com/cruk-microarray)

Galaxy tools for metabolomics maintained by Workflow4Metabolomics

A course on Analysing Next Generation (/High Throughput etc..) Sequencing data using Bioconductor

tidy processing of biological sequences in R

circtools: a modular, python-based framework for circRNA-related tools that unifies several functionalities in a single, command line driven software.

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

A Comet-based, best practices proteomics pipeline.

RawTools is an open-source and freely available package designed to perform scan data parsing and quantification, and quality control analysis of Thermo Orbitrap raw mass spectrometer files from data-dependent acquisition experiments.

Interpretation of proteomics identification results

Computable build reports, package metadata, and download stats from the Bioconductor project

SIRIUS is a software for discovering a landscape of de-novo identification of metabolites using tandem mass spectrometry. This repository contains the code of the SIRIUS Software (GUI and CLI)

Conversion between scRNA-seq objects