• Stars
    star
    1
  • Language
    Java
  • Created over 9 years ago
  • Updated over 7 years ago

Reviews

There are no reviews yet. Be the first to send feedback to the community and the maintainers!

Repository Details

Manipulating fasta sequence databases

More Repositories

1

ThermoRawFileParser

Thermo RAW file parser that runs on Linux/Mac and all other platforms that support Mono
C#
183
star
2

DeepLC

DeepLC: Retention time prediction for (modified) peptides using Deep Learning.
Python
52
star
3

peptide-shaker

Interpretation of proteomics identification results
Java
47
star
4

ms2rescore

Modular and user-friendly platform for AI-assisted rescoring of peptide identifications
Python
40
star
5

searchgui

Highly adaptable common interface for proteomics search and de novo engines
Java
39
star
6

ms2pip

MS²PIP: Fast and accurate peptide spectrum prediction for multiple fragmentation methods, instruments, and labeling techniques.
HTML
38
star
7

moFF

A modest Feature Finder (moFF) to extract MS1 intensities from Thermo raw file
Python
33
star
8

compomics-utilities

Open source Java library for computational proteomics
Java
30
star
9

meta-proteome-analyzer

MetaProteomeAnalyzer (MPA) software for analyzing and visualizing MS-based metaproteomics data.
TSQL
27
star
10

psm_utils

Common utilities for parsing and handling peptide-spectrum matches and search engine results in Python
Python
24
star
11

ThermoRawFileParserGUI

Graphical user interface for the ThermoRawFileParser
Java
18
star
12

denovogui

Graphical user interface for de novo sequencing of tandem mass spectra
Java
14
star
13

spectrum_similarity

Scoring functions to compare MS/MS spectra
Java
10
star
14

jsparklines

Sparklines for java tables
Java
8
star
15

COSS

COSS: CompOmics Spectral Searching
Java
8
star
16

workshop-ml-proteomics

Workshop: Tackling peptide identification ambiguity with machine learning
Jupyter Notebook
8
star
17

scop3d

Sequence conservation of protein on 3D structure.
Python
7
star
18

CALLC

Python
6
star
19

cellmissy

Cell Migration Invasion Storage System.
Java
6
star
20

lesSDRF

Jupyter Notebook
5
star
21

pout2prot

Pout2Prot converts Percolator output files to protein group and subgroup files using Occam's razor or anti-Occam's razor. These output files can directly be used in Prophane for further downstream taxonomic and functional analysis
Python
5
star
22

pladipus

Platform for Distributed Proteomics Software
Java
4
star
23

colims

A lims system to automate and expedite proteomics data management, processing and analysis.
APL
4
star
24

reporter

Protein quantification based on reporter ions
Java
4
star
25

IM2Deep

Collisional cross-section prediction for modified peptides
Python
4
star
26

fragmentation-analyzer

A standalone java tool for analyzing ms/ms fragmentation data.
Java
4
star
27

thermo-msf-parser

Parser and viewer for thermo msf files.
Java
3
star
28

mascotdatfile

Java API for MS/MS search results by Mascot (Matrix Science).
Java
3
star
29

icelogo

Next-generation visualization of protein consensus sequences by iceLogo.
Java
3
star
30

xilmass

An algorithm to identify cross-linked peptides
Java
3
star
31

ms-lims

Mass spectrometry based proteomics information management system.
Java
2
star
32

mumble

Finding the perfect modification for your mass shift
Python
2
star
33

ms2rescore-rs

Rust functionality for the MS²Rescore package
Rust
2
star
34

moff-gui

A graphical user interface for the Modest Feature Finding algorithm (moFF)
Java
2
star
35

CellMojo

Python
2
star
36

mitraq

Multiple iTRAQ/TMT Data Analysis
Java
1
star
37

xtandem-parser

Java-based parser for X!Tandem output xml files
Java
1
star
38

pride-asa-pipeline

Uniform annotation of identified spectra.
Java
1
star
39

tabloidProteome

HTML
1
star
40

elude-jwrapper

A Java API to make use of the retention time prediction functionality from elude.
Java
1
star
41

CompPyTools

Small Python scripts developed in the CompOmics group
Python
1
star
42

ReSpinOnline

Online public viewer for ReSpin Results
HTML
1
star
43

spectrawl

A rich client tool used for browsing through spectra looking for specific mass differences.
Java
1
star
44

QuantPridePep

Pipeline to bring peptdie quantification in Pride using moFF
Python
1
star
45

search-all-assess-subset

An implementation of the Search All, Asses Subset strategy for FDR estimation in shotgun proteomics.
HTML
1
star
46

Tissue_prediction_manuscript

Jupyter Notebook
1
star