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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
ProteoBench
8 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 OpenMS
33 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 Proteomics
18 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 Proteomics
8 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
pGlyco
1 version - Latest release: about 1 month ago - 223 downloads last month - 1 maintainer
benppy 1.0.7
BayesENproteomics in Python
7 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 Toolkit
13 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 utilities
35 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 UniProt
1 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 proteomics
10 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
mokapot 0.10.0
Fast and flexible semi-supervised learning for peptide detection
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
sagepy 0.2.8
Proteomics search & quantification so fast that it feels like magic
10 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
pypdb 2.4
A Python wrapper for the RCSB Protein Data Bank (PDB) API
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
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 Aligner
2 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
peptdeep 1.1.9
The AlphaX deep learning framework for Proteomics
33 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 package
17 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
alphatims 1.0.8
A Python package to index Bruker TimsTOF raw data for fast and easy accession and visualization
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
Top 9.6% on pypi.org
alphabase 1.2.3
An infrastructure Python package of the AlphaX ecosystem
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
pdeep 0.0.1
pDeep
1 version - Latest release: 7 days ago - 1 maintainer
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 library
2 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-mobilities
4 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 data
9 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 predictor
4 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 data
4 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 ecosystem
11 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 data
4 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 Uploader
5 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/MS
8 versions - Latest release: over 7 years ago - 2 dependent repositories - 26 downloads last month - 1 maintainer
simsalabim 0.2.0
Simple Interface for MS Applications
2 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
SAMPEI
9 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 spectra
5 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 files
12 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 PCA
3 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 analysis
1 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 interface
1 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 data
6 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 proteogenomics
21 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 engine
2 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 analysis
5 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 Networks
11 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 Interactomes
4 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 proteins
2 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 analysis
2 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 framework
20 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 peptides
1 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 APIs
21 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 peptides
4 versions - Latest release: 10 months ago - 41 downloads last month - 1 stars on GitHub - 1 maintainer
calisp 3.0.13
Isotope analysis of proteomics data
10 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 models
4 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 experiments
26 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 cobrapy
11 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
sdrf-pipelines 0.0.26
Translate, convert SDRF to configuration pipelines
24 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 generator
1 version - Latest release: about 1 month ago - 164 downloads last month - 5 stars on GitHub - 1 maintainer
Top 8.7% on pypi.org
triqler 0.7.3
Triqler: TRansparent Identification-Quantification-Linked Error Rates
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
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 output
16 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 data
59 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 turnover
1 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 Engine
5 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 Selection
10 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 API
1 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
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 ecosystem
9 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 Data
8 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
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 data
10 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 format
1 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