Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
pypi.org "proteomics" keyword
alphapept 0.5.3
A modular, python-based framework for mass spectrometry.18 versions - Latest release: about 1 month ago - 366 downloads last month - 137 stars on GitHub - 1 maintainer
proteobench 0.2.7b0
ProteoBench8 versions - Latest release: 3 days ago - 154 downloads last month - 27 stars on GitHub - 1 maintainer
pyopenms-nightly 2.6.0.dev20201012 💰
Python wrapper for C++ LCMS library OpenMS33 versions - Latest release: over 3 years ago - 1 dependent repositories - 1.51 thousand downloads last month - 455 stars on GitHub - 1 maintainer
pygeno 2.0.0
A python package for Personalized Genomics and Proteomics18 versions - Latest release: about 4 years ago - 1 dependent repositories - 127 downloads last month - 307 stars on GitHub - 2 maintainers
dlomix 0.1.0
Deep Learning for Proteomics8 versions - Latest release: 16 days ago - 1 dependent package - 1 dependent repositories - 172 downloads last month - 17 stars on GitHub - 1 maintainer
pglyco 0.0.1
pGlyco1 version - Latest release: about 1 month ago - 223 downloads last month - 1 maintainer
benppy 1.0.7
BayesENproteomics in Python7 versions - Latest release: over 5 years ago - 1 dependent repositories - 82 downloads last month - 3 stars on GitHub - 1 maintainer
secat 1.1.5
Size-Exclusion Chromatography Algorithmic Toolkit13 versions - Latest release: 12 months ago - 1 dependent repositories - 63 downloads last month - 5 stars on GitHub - 1 maintainer
nmdc-schema 10.3.0
Schema resources for the National Microbiome Data Collaborative (NMDC)73 versions - Latest release: 4 days ago - 3.16 thousand downloads last month - 26 stars on GitHub - 4 maintainers
msstitch 3.15
MS proteomics post processing utilities35 versions - Latest release: 6 months ago - 2 dependent repositories - 203 downloads last month - 5 stars on GitHub - 1 maintainer
favapy 1.0.1
Infer Functional Associations using Variational Autoencoders on -Omics data.22 versions - Latest release: 3 days ago - 1 dependent repositories - 227 downloads last month - 33 stars on GitHub - 1 maintainer
proteo 1.0.1
A simple client library for UniProt1 version - Latest release: about 5 years ago - 1 dependent repositories - 19 downloads last month - 1 stars on GitHub - 1 maintainer
camprot 0.0.13
camprot: Tools for Computational proteomics10 versions - Latest release: about 7 years ago - 1 dependent repositories - 51 downloads last month - 0 stars on GitHub - 1 maintainer
xirt 1.2.41
xiRT: Multi-dimensional Retention Time Prediction for Linear and Crosslinked Peptides.14 versions - Latest release: about 3 years ago - 1 dependent repositories - 146 downloads last month - 8 stars on GitHub - 1 maintainer
Top 7.6% on pypi.org
26 versions - Latest release: 8 months ago - 5 dependent packages - 4 dependent repositories - 1.15 thousand downloads last month - 36 stars on GitHub - 1 maintainer
mokapot 0.10.0
Fast and flexible semi-supervised learning for peptide detection26 versions - Latest release: 8 months ago - 5 dependent packages - 4 dependent repositories - 1.15 thousand downloads last month - 36 stars on GitHub - 1 maintainer
sagepy 0.2.8
Proteomics search & quantification so fast that it feels like magic10 versions - Latest release: 13 days ago - 1 dependent package - 73 downloads last month - 192 stars on GitHub - 1 maintainer
Top 3.7% on pypi.org
19 versions - Latest release: 4 days ago - 6 dependent packages - 21 dependent repositories - 1.44 thousand downloads last month - 289 stars on GitHub - 1 maintainer
pypdb 2.4
A Python wrapper for the RCSB Protein Data Bank (PDB) API19 versions - Latest release: 4 days ago - 6 dependent packages - 21 dependent repositories - 1.44 thousand downloads last month - 289 stars on GitHub - 1 maintainer
im2deep 0.1.6
Framework for prediction of collisional cross-section of peptides.7 versions - Latest release: about 1 month ago - 1 dependent package - 354 downloads last month - 2 stars on GitHub - 1 maintainer
ssw 0.4.1
Smith-Waterman Sequence Aligner2 versions - Latest release: about 5 years ago - 2 dependent packages - 5 dependent repositories - 61 downloads last month - 34 stars on GitHub - 1 maintainer
psm-utils 0.9.0
Common utilities for parsing and handling peptide-spectrum matches and search engine results.24 versions - Latest release: 18 days ago - 4 dependent packages - 1.48 thousand downloads last month - 20 stars on GitHub - 2 maintainers
Top 9.8% on pypi.org
33 versions - Latest release: about 1 month ago - 2 dependent packages - 2 dependent repositories - 743 downloads last month - 79 stars on GitHub - 2 maintainers
peptdeep 1.1.9
The AlphaX deep learning framework for Proteomics33 versions - Latest release: about 1 month ago - 2 dependent packages - 2 dependent repositories - 743 downloads last month - 79 stars on GitHub - 2 maintainers
peptacular 2.0.0
A spectacularly simple package for working with peptide sequences.14 versions - Latest release: about 1 month ago - 2 dependent packages - 1 dependent repositories - 147 downloads last month - 8 stars on GitHub - 1 maintainer
multiplierz 2.2.2
The MultiplierZ proteomics package17 versions - Latest release: about 1 month ago - 2 dependent packages - 2 dependent repositories - 284 downloads last month - 21 stars on GitHub - 2 maintainers
deeplc 2.2.36
DeepLC: Retention time prediction for (modified) peptides using Deep Learning.93 versions - Latest release: about 1 month ago - 2 dependent packages - 1 dependent repositories - 1.77 thousand downloads last month - 46 stars on GitHub - 3 maintainers
Top 7.9% on pypi.org
20 versions - Latest release: 10 months ago - 3 dependent packages - 3 dependent repositories - 2.07 thousand downloads last month - 69 stars on GitHub - 2 maintainers
alphatims 1.0.8
A Python package to index Bruker TimsTOF raw data for fast and easy accession and visualization20 versions - Latest release: 10 months ago - 3 dependent packages - 3 dependent repositories - 2.07 thousand downloads last month - 69 stars on GitHub - 2 maintainers
Top 9.6% on pypi.org
27 versions - Latest release: about 2 months ago - 4 dependent packages - 3 dependent repositories - 1.17 thousand downloads last month - 23 stars on GitHub - 2 maintainers
alphabase 1.2.3
An infrastructure Python package of the AlphaX ecosystem27 versions - Latest release: about 2 months ago - 4 dependent packages - 3 dependent repositories - 1.17 thousand downloads last month - 23 stars on GitHub - 2 maintainers
seer-pas-sdk 0.1.0
SDK for Seer Proteograph Analysis Suite (PAS)1 version - Latest release: about 2 months ago - 53 downloads last month - 0 stars on GitHub - 1 maintainer
alpaca-proteomics 0.9.980
Absolute Protein Quantification python library2 versions - Latest release: about 2 months ago - 196 downloads last month - 0 stars on GitHub - 1 maintainer
rustyms 0.8.3
A library to handle proteomic mass spectrometry data and match peptides to spectra.2 versions - Latest release: 2 months ago - 361 downloads last month - 10 stars on GitHub - 1 maintainer
cpred 0.0.11
CPred: A deep learning framework for predicting the charge state distribution in modified and unm...9 versions - Latest release: 3 months ago - 57 downloads last month - 0 stars on GitHub - 1 maintainer
profasta 0.0.5
A Python library for working with protein containing FASTA files.5 versions - Latest release: about 1 month ago - 180 downloads last month - 0 stars on GitHub - 1 maintainer
xi-mzidentml-converter 0.1.29
xi-mzidentml-converter uses pyteomics (https://pyteomics.readthedocs.io/en/latest/index.html) to ...26 versions - Latest release: 19 days ago - 840 downloads last month - 0 stars on GitHub - 1 maintainer
pixelgen-pixelator 0.16.2
A command-line tool and library to process and analyze sequencing data from Molecular Pixelation ...8 versions - Latest release: 2 months ago - 100 downloads last month - 9 stars on GitHub - 3 maintainers
ionmob 0.2.2
predict peptide collision-cross sections / ion-mobilities4 versions - Latest release: 8 months ago - 1 dependent package - 21 downloads last month - 10 stars on GitHub - 1 maintainer
detelpy 0.1.13
Python package of the deTEL translation error detection pipeline from mass-spectrometry data9 versions - Latest release: 2 months ago - 225 downloads last month - 106 stars on GitHub - 2 maintainers
flimsay 0.4.0
A super simple fast IMS predictor4 versions - Latest release: 10 months ago - 37 downloads last month - 1 stars on GitHub - 1 maintainer
proteomics-downstream-analysis 0.1.3
A package for downstream data analysis of proteomics data4 versions - Latest release: 11 months ago - 43 downloads last month - 0 stars on GitHub - 1 maintainer
fastaframes 1.1.0
A very simple fasta file parser.5 versions - Latest release: 8 months ago - 50 downloads last month - 2 stars on GitHub - 1 maintainer
directlfq 0.2.19
An open-source Python package of the AlphaPept ecosystem11 versions - Latest release: about 1 month ago - 511 downloads last month - 32 stars on GitHub - 1 maintainer
synthedia 1.0.3
Generate synthetic DIA LC-MS/MS proteomics data4 versions - Latest release: about 1 year ago - 31 downloads last month - 7 stars on GitHub - 1 maintainer
clumps-ptm 0.0.6
CLUMPS-PTM driver gene discovery using 3D protein structure (Getz Lab).7 versions - Latest release: about 1 year ago - 87 downloads last month - 6 stars on GitHub - 1 maintainer
pyproteininference 1.0.0
Python Package for running custom protein inference algorithms on tab-formatted tandem MS/MS sear...1 version - Latest release: almost 2 years ago - 18 downloads last month - 0 stars on GitHub - 1 maintainer
uniprotscraper 0.3
UniprotScraper is a web scraping tool that specialized for Uniprot Database.3 versions - Latest release: over 2 years ago - 1 dependent repositories - 10 downloads last month - 4 stars on GitHub - 1 maintainer
stirplate 1.4.0
Stirplate Data Uploader5 versions - Latest release: over 7 years ago - 2 dependent repositories - 18 downloads last month - 0 stars on GitHub - 1 maintainer
sixgill 0.2.4
six-frame genome-inferred libraries for LC-MS/MS8 versions - Latest release: over 7 years ago - 2 dependent repositories - 26 downloads last month - 1 maintainer
simsalabim 0.2.0
Simple Interface for MS Applications2 versions - Latest release: almost 2 years ago - 1 dependent repositories - 25 downloads last month - 2 stars on GitHub - 1 maintainer
seq-to-first-iso 1.1.0
Compute first two isotopologues intensity from peptide sequence.12 versions - Latest release: over 4 years ago - 1 dependent repositories - 51 downloads last month - 0 stars on GitHub - 2 maintainers
sampei 0.0.9
SAMPEI9 versions - Latest release: almost 4 years ago - 1 dependent repositories - 27 downloads last month - 4 stars on GitHub - 2 maintainers
riana 0.7.2
riana integrates the relative abundance of isotopomers in mass spectra5 versions - Latest release: about 1 year ago - 1 dependent repositories - 18 downloads last month - 4 stars on GitHub - 1 maintainer
rawquant 0.2.3
Package for extracting scan meta data and quantification information from Thermo .raw files12 versions - Latest release: almost 6 years ago - 1 dependent repositories - 39 downloads last month - 10 stars on GitHub - 1 maintainer
ratvec 0.1.2
Generating dense embeddings for proteins using kernel PCA3 versions - Latest release: about 5 years ago - 1 dependent repositories - 33 downloads last month - 4 stars on GitHub - 3 maintainers
pytrapment 1.0.1
pytrapment: create an entrapment database for proteomic mass spectrometry analysis1 version - Latest release: about 3 years ago - 1 dependent repositories - 8 downloads last month - 1 stars on GitHub - 1 maintainer
pyrawr 0.1.0
Python wrapper around the ThermoRawFileParser command line interface1 version - Latest release: about 3 years ago - 1 dependent repositories - 24 downloads last month - 1 stars on GitHub - 2 maintainers
pyqms 0.6.5
pyQms - Python module for accurate quantification of mass spectrometry data6 versions - Latest release: about 2 years ago - 3 dependent repositories - 54 downloads last month - 28 stars on GitHub - 4 maintainers
pypgatk 0.0.24
Python tools for proteogenomics21 versions - Latest release: 30 days ago - 1 dependent repositories - 371 downloads last month - 9 stars on GitHub - 1 maintainer
pymzid 0.3.2
pymzid reads in mzidentml files from proteomics search engine2 versions - Latest release: almost 4 years ago - 1 dependent repositories - 19 downloads last month - 1 stars on GitHub - 1 maintainer
pymultiomics 1.0.4
A Python package for multi-omics data integration and analysis5 versions - Latest release: about 2 years ago - 1 dependent repositories - 164 downloads last month - 15 stars on GitHub - 1 maintainer
pout2prot 1.3.0
A script to perform protein grouping on pout-files (generated by Percolator).8 versions - Latest release: over 2 years ago - 1 dependent repositories - 32 downloads last month - 4 stars on GitHub - 1 maintainer
photon-ptm 0.3.1
PHOsphoproteomic dissecTiOn via Networks11 versions - Latest release: about 5 years ago - 1 dependent repositories - 33 downloads last month - 17 stars on GitHub - 1 maintainer
param-medic 0.2
Param-Medic optimizes MS/MS search parameter settings.1 version - Latest release: over 7 years ago - 1 dependent repositories - 13 downloads last month - 3,229 stars on GitHub - 1 maintainer
omicsintegrator 2.3.10
Prize-Collecting Steiner Forests for Interactomes4 versions - Latest release: over 5 years ago - 1 dependent repositories - 42 downloads last month - 49 stars on GitHub - 1 maintainer
motiffinder 0.0.2
A novel approach to motif identification in proteins2 versions - Latest release: almost 5 years ago - 1 dependent repositories - 23 downloads last month - 1 stars on GitHub - 1 maintainer
maspy 1.1.3
An open-source python library for mass spectrometry-based proteomics data analysis2 versions - Latest release: over 7 years ago - 2 dependent repositories - 8 downloads last month - 2 stars on GitHub - 1 maintainer
magine 0.1.5
Package to analyze biological data.20 versions - Latest release: about 3 years ago - 2 dependent repositories - 150 downloads last month - 9 stars on GitHub - 1 maintainer
lightdock 0.9.4 💰
A macromolecular docking framework20 versions - Latest release: 10 months ago - 1 dependent repositories - 527 downloads last month - 259 stars on GitHub - 1 maintainer
isoelectric 1.0
IPC (Isoelectric Point Calculator) - prediction of isoelectric point of proteins and peptides1 version - Latest release: over 4 years ago - 1 dependent repositories - 54 downloads last month - 1 maintainer
enrich-omics 0.2.1
Package to perform enrichment analysis in python using EnrichR and OpenTargets APIs21 versions - Latest release: about 2 years ago - 1 dependent repositories - 121 downloads last month - 16 stars on GitHub - 1 maintainer
antibp3 1.3
A tool to predict anti-bacterial peptides4 versions - Latest release: 10 months ago - 41 downloads last month - 1 stars on GitHub - 1 maintainer
calisp 3.0.13
Isotope analysis of proteomics data10 versions - Latest release: 9 months ago - 1 dependent repositories - 98 downloads last month - 3 stars on GitHub - 1 maintainer
berteome 0.1.6 💰
A library to analyze and explore protein sequences using BERT models4 versions - Latest release: over 2 years ago - 1 dependent repositories - 50 downloads last month - 3 stars on GitHub - 1 maintainer
picked-group-fdr 0.7.1
Scalable, accurate and sensitive protein group FDRs for large-scale mass spectrometry experiments26 versions - Latest release: 8 days ago - 205 downloads last month - 6 stars on GitHub - 1 maintainer
patpat 1.1.1
Patpat is public proteomics dataset search framework that only requires protein identifiers to be...6 versions - Latest release: about 1 year ago - 35 downloads last month - 6 stars on GitHub - 1 maintainer
depthcharge-ms 0.4.8
A mass spectrometry toolkit for deep learning with Transformer models.17 versions - Latest release: 10 days ago - 2 dependent packages - 1 dependent repositories - 1.1 thousand downloads last month - 51 stars on GitHub - 1 maintainer
geckopy 2.0.2
Methods for using the GECKO model with cobrapy11 versions - Latest release: about 3 years ago - 1 dependent repositories - 152 downloads last month - 61 stars on GitHub - 2 maintainers
Top 7.8% on pypi.org
24 versions - Latest release: about 1 month ago - 1 dependent package - 3 dependent repositories - 232 downloads last month - 13 stars on GitHub - 1 maintainer
sdrf-pipelines 0.0.26
Translate, convert SDRF to configuration pipelines24 versions - Latest release: about 1 month ago - 1 dependent package - 3 dependent repositories - 232 downloads last month - 13 stars on GitHub - 1 maintainer
mopepgen 1.4.0
Multi-omic peptide generator1 version - Latest release: about 1 month ago - 164 downloads last month - 5 stars on GitHub - 1 maintainer
Top 8.7% on pypi.org
20 versions - Latest release: 5 months ago - 3 dependent packages - 3 dependent repositories - 1.64 thousand downloads last month - 18 stars on GitHub - 1 maintainer
triqler 0.7.3
Triqler: TRansparent Identification-Quantification-Linked Error Rates20 versions - Latest release: 5 months ago - 3 dependent packages - 3 dependent repositories - 1.64 thousand downloads last month - 18 stars on GitHub - 1 maintainer
simsi-transfer 0.6.1
Software-assisted reduction of missing values in phosphoproteomics and proteomics isobaric labeli...18 versions - Latest release: about 1 month ago - 1 dependent repositories - 193 downloads last month - 2 stars on GitHub - 2 maintainers
pytmt 0.5.0
pytmt returns ms2 tmt quantification values from Crux Percolator output16 versions - Latest release: 8 months ago - 1 dependent repositories - 25 downloads last month - 2 stars on GitHub - 1 maintainer
cptac 1.5.13
Python packaging for CPTAC data59 versions - Latest release: 3 months ago - 1 dependent repositories - 673 downloads last month - 79 stars on GitHub - 2 maintainers
splat-workflow 0.1.0
simultaneous proteome localization and turnover1 version - Latest release: over 1 year ago - 9 downloads last month - 2 stars on GitHub - 1 maintainer
albion-similog 0.3.7
Compute a consensus dataseries with FAMSA algorithm.12 versions - Latest release: almost 2 years ago - 98 downloads last month - 126 stars on GitHub - 1 maintainer
pepid 1.2.0
Pepid: a Highly Modifiable, Bioinformatics-Oriented Peptide Search Engine5 versions - Latest release: 10 months ago - 28 downloads last month - 2 stars on GitHub - 1 maintainer
protexam 0.9.1
Inspect your quantitative proteomics results using this streamlit-powered dashboard. The app is s...1 version - Latest release: about 2 years ago - 1 dependent repositories - 16 downloads last month - 1 stars on GitHub - 1 maintainer
proms 1.0.12
Protein Markers Selection10 versions - Latest release: about 1 year ago - 1 dependent repositories - 65 downloads last month - 6 stars on GitHub - 1 maintainer
pridepy 0.0.2
Python Client library for PRIDE Rest API1 version - Latest release: over 3 years ago - 1 dependent repositories - 39 downloads last month - 14 stars on GitHub - 1 maintainer
Top 9.4% on pypi.org
27 versions - Latest release: 4 months ago - 1 dependent package - 8 dependent repositories - 2.41 thousand downloads last month - 4 stars on GitHub - 2 maintainers
protmapper 0.0.29
Map protein sites to human reference sequence.27 versions - Latest release: 4 months ago - 1 dependent package - 8 dependent repositories - 2.41 thousand downloads last month - 4 stars on GitHub - 2 maintainers
pydiaid 0.0.23
An open-source Python package of the AlphaPept ecosystem9 versions - Latest release: 4 months ago - 1 dependent repositories - 75 downloads last month - 14 stars on GitHub - 1 maintainer
dart-id 2.0.7
RT Alignment and Peptide ID Confidence Updating for LC-MS/MS Data8 versions - Latest release: over 4 years ago - 1 dependent repositories - 88 downloads last month - 12 stars on GitHub - 1 maintainer
Top 7.3% on pypi.org
74 versions - Latest release: about 1 year ago - 2 dependent packages - 4 dependent repositories - 269 downloads last month - 27 stars on GitHub - 2 maintainers
pyprophet 2.2.5
PyProphet: Semi-supervised learning and scoring of OpenSWATH results.74 versions - Latest release: about 1 year ago - 2 dependent packages - 4 dependent repositories - 269 downloads last month - 27 stars on GitHub - 2 maintainers
ms2rescore 3.0.3
MS²Rescore: Sensitive PSM rescoring with predicted MS² peak intensities and retention times.28 versions - Latest release: about 1 month ago - 1 dependent repositories - 681 downloads last month - 38 stars on GitHub - 2 maintainers
alphamap 0.1.10
Peptide level analysis of bottom-up proteomics data10 versions - Latest release: about 2 years ago - 87 downloads last month - 67 stars on GitHub - 2 maintainers
alphaviz 1.1.15
A interactive Dashboard to explore mass spectrometry data.15 versions - Latest release: almost 2 years ago - 1 dependent repositories - 86 downloads last month - 27 stars on GitHub - 1 maintainer
quantmsio 0.0.3
Convert multiple files into quantms.io format1 version - Latest release: about 1 month ago - 214 downloads last month - 5 stars on GitHub - 1 maintainer
alphastats 0.6.5
An open-source Python package for automated and scalable statistical analysis of mass spectrometr...31 versions - Latest release: 9 months ago - 1 dependent repositories - 446 downloads last month - 41 stars on GitHub - 1 maintainer
Related Keywords
mass-spectrometry
33
bioinformatics
32
python
20
mass spectrometry
15
protein
11
genomics
10
machine-learning
9
deep-learning
7
peptides
6
metabolomics
6
biology
5
peptide
5
software
5
scientific
4
quantification
4
peptide-identification
4
timsTOF
4
visualization
4
machine learning
4
kinetics
3
cancer
3
transcriptomics
3
Proteomics
3
multiomics
3
fasta
3
proteomics-data-analysis
3
deep learning
3
spectrometry
3
ms
3
bruker
3
proteogenomics
3
ms-data
3
turnover
2
computational-biology
2
DeepLC
2
alignment
2
python3
2
data-independent-acquisition
2
protein-inference
2
omics
2
swath-ms
2
pytorch
2
phosphorylation
2
AlphaX ecosystem
2
retention time
2
alphapept-ecosystem
2
AlphaPept ecosystem
2
chemistry
2
proteins
2
Bioinformatics
2
data-integration
2
multi-omics
2
cancer-genomics
2
uniprot
2
ensembl
2
data
2
ion-mobility
2
gui
2
metaproteomics
2
dia
2
dna
2
percolator
2
algorithms
2
vcf
2
sequence
2
framework
2
missing values
2
peptide-sequences
2
crosslinking
2
protein-sequences
2
retention-time
2
protein-structure
2
artificial-intelligence
1
Percolator
1
rnaseq
1
maxquant
1
network analysis
1
thermorawfileparser
1
pI
1
isoelectric point
1
dia-nn
1
swarm-intelligence
1
structural-biology
1
structural-bioinformatics
1
fragpipe
1
protein-protein-interaction
1
protein-docking
1
protein-dna-interactions
1
protein-design
1
molecular-structures
1
molecular-biology
1
glowworm-swarm-optimization
1
docking
1
bioinformatics-tool
1
raw
1
ThermoRawFileParser
1
statistics
1
representation-learning
1
nlp
1
kernel-pca
1