Pinned Repositories
DLEAMSE
A Deep LEArning-based Mass Spectra Embedder for spectral similarity scoring
ibaqpy
Absolute quantification package based on quantms.io
nf-workflows
Repository of Nextflow+BioContainers workflows
pIR
Estimation of isoelectric point of peptides and proteins using support vector machines (SVM).
pmultiqc
A library for QC report based on MultiQC framework
proteomics-sample-metadata
The Proteomics sample metadata: Standard for experimental design annotation in proteomics datasets
py-pgatk
Python tools for proteogenomics analysis toolkit
quantms
Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.
quantms.io
The proteomics quantification format, extending mzTab for large scale datasets.
sdrf-pipelines
A repository to convert SDRF proteomics files into pipelines config files
BigBio Stack's Repositories
bigbio/proteomics-sample-metadata
The Proteomics sample metadata: Standard for experimental design annotation in proteomics datasets
bigbio/quantms
Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.
bigbio/sdrf-pipelines
A repository to convert SDRF proteomics files into pipelines config files
bigbio/pmultiqc
A library for QC report based on MultiQC framework
bigbio/ibaqpy
Absolute quantification package based on quantms.io
bigbio/py-pgatk
Python tools for proteogenomics analysis toolkit
bigbio/DLEAMSE
A Deep LEArning-based Mass Spectra Embedder for spectral similarity scoring
bigbio/quantms.io
The proteomics quantification format, extending mzTab for large scale datasets.
bigbio/quantms-utils
A python library with scripts and helpers classes for quantms workflow
bigbio/qccalculator
Development for python driven QC calculation (QCCalculator)
bigbio/diann-docker
DIANN docker container based on the linux version from DIANN
bigbio/fslite
Lightweight Feature selection Python library
bigbio/pgatk-io
High performance io library for proteogenomics
bigbio/pgt-pangenome
Protegenomics analysis based on Pangenome references
bigbio/spectrafuse
Incremental clustesting pipeline from quantms data.
bigbio/pyspectrafuse
Python library with utility scripts for spectrafuse pipeline
bigbio/.github
bigbio/hvantk
Hail variant annotation toolkit
bigbio/lucXor
JAVA-based implementation of LuciPHOr that can process any variable PTM.
bigbio/mad_decoy
Mad decoy is a decoy simulation tool to assess large-scale merge of q-values.
bigbio/msgfplus
MS-GF+ (aka MSGF+ or MSGFPlus) performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database.
bigbio/openmsrescore
OpenMS MSRescore tool, integration tool between MS2Rescore and OpenMS
bigbio/pia
:books: :microscope: PIA - Protein Inference Algorithms
bigbio/quantms-rescoring
quantms and ms2rescore helper functions and scripts
bigbio/quantms-test-datasets
bigbio/quantms.org
Web page storing all the datasets renalyzed with quantms
bigbio/sage
Proteomics searching so fast it feels like magic
bigbio/sdrf-cellline-metadata-db
SDRF Cell Line Metadata Database
bigbio/sdrf-utils
sdrf-cls
bigbio/tdf2mzml
quantms bruker to mzml