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Search results for protein proteomics
protein
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proteomics
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50 search results found
Pypdb
⭐
258
A Python API for the RCSB Protein Data Bank (PDB)
Pygeno
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242
Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
Lightdock
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234
Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm
Diann
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152
DIA-NN - a universal automated software suite for DIA proteomics data analysis.
Philosopher
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104
A complete toolkit for shotgun proteomics data analysis
Famsa
⭐
101
Algorithm for ultra-scale multiple sequence alignments (3M protein sequences in 5 minutes and 24 GB of RAM)
Plass
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99
Protein-Level ASSembler (PLASS): sensitive and precise protein assembler
Metamorpheus
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81
Proteomics search software with integrated calibration, PTM discovery, bottom-up, top-down and LFQ capabilities
Pyfeat
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68
A Python-based Effective Feature Generation Tool from DNA, RNA, and Protein Sequences
Awesome Structural Bioinformatics
⭐
54
Structural Bioinformatics is awesome. Throw your textbook in the garbage, light the garbage can on fire, and blend the ashes into your cold brew almond milk latte and read this.
Protti
⭐
50
Picotti lab data analysis package.
Peptide Shaker
⭐
41
Interpretation of proteomics identification results
Proteus
⭐
36
R package for analysing proteomics data
Deep Proteomics
⭐
33
Babelomics
⭐
31
Lfq Analyst
⭐
27
The repo for LFQ-Analyst
Long Read Proteogenomics
⭐
26
A workflow for enhanced protein isoform detection through integration of long-read RNA-seq and mass spectrometry-based proteomics.
Omicsintegrator2
⭐
20
Prize-Collecting Steiner Forests for Interactomes
Pia
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20
📚 🔬 PIA - Protein Inference Algorithms
Paw_pipeline
⭐
18
A Comet-based, best practices proteomics pipeline.
Protigy
⭐
17
Proteomics Toolset for Integrative Data Analysis
Plink2
⭐
17
pLink is a software dedicated for the analysis of chemically cross-linked proteins or protein complexes using mass spectrometry.
Pride Inspector
⭐
15
PRIDE Inspector is a Java desktop application to visualise and Quality Assessment on Mass Spectrometry data and Proteomics
Iq
⭐
15
An R package to estimate relative protein abundances from ion quantification in DIA-MS-based proteomics
Meta Proteome Analyzer
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14
MetaProteomeAnalyzer (MPA) software for analyzing and visualizing MS-based metaproteomics data.
Pfind3
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12
Sdrf Pipelines
⭐
12
A repository to convert SDRF proteomics files into pipelines config files
Photon
⭐
11
PHOsphoproteomic dissecTiOn using Networks
Mmtf Proteomics
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11
Methods for mapping proteomics data on 3D protein structure.
Sequence Database Curator
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10
This program dereplicates and/or filter nucleotide and/or protein database from a list of names or sequences (by exact match).
Deeppep
⭐
10
Deep proteome inference from peptide profiles
Secretsanta
⭐
9
flexible pipelines for scalable secretome prediction, R package
Isobar
⭐
9
isobar - R library for the Analysis and quantitation of isobarically tagged MSMS proteomics data
Workflow Testing
⭐
8
Automated testing of workflows against Galaxy
Hitmap
⭐
8
An R package of High-resolution Informatics Toolbox for Maldi-imaging Proteomics
Phage Host Prediction
⭐
7
Published in PLOS ONE. We show that using embeddings of receptor-binding proteins presents improvements over handcrafted genomic and protein sequence features for phage-host interaction prediction — with the highest performance obtained using the transformer-based protein language model ProtT5
Nf Workflows
⭐
7
Repository of Nextflow+BioContainers workflows
Inf
⭐
7
SCALLOP-INF analysis
Splicevista
⭐
6
Splice variant analysis in shotgun proteomics data
Peptagram
⭐
6
HTML5 interactive visualisations of proteomic experiments
Uniprot Mongodb
⭐
6
Spritz
⭐
6
Software for RNA-Seq analysis to create sample-specific proteoform databases from RNA-Seq data
Msstatsconvert
⭐
6
Converter functions for the MSstats package
Pixelator
⭐
6
A command-line tool and library to process and analyze sequencing data from Molecular Pixelation (MPX) assays.
Scavager
⭐
5
Peptacular
⭐
5
A spectacularly simple package for working with peptide sequences.
Rcpa.tools
⭐
5
Proteomics Tools Suite
Unimod
⭐
5
Amino acid modifications for mass spectrometry
Proteinclusterquant
⭐
5
Protein Cluster Quant is a Java software for the analysis of complex proteomics samples (quantitative or not). It helps to reduce the redundancy of the peptide-to-protein relationship and to visualize the results in a bipartite network (Cytoscape).
Dia Umpire
⭐
5
Computational analysis for mass spectrometry-based proteomics data
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