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sigora - Signature Over-Representation Analysis

Pathway analysis is a method of statistically linking observations on the molecular level to biological processes or pathways on the systems (i.e., organism, organ, tissue, cell) level. Traditionally, pathway analysis methods regard pathways as collections of single genes and treat all genes in a pathway as equally informative. However, this can lead to identifying spurious pathways as statistically significant since components are often shared amongst pathways. SIGORA seeks to avoid this pitfall by focusing on genes or gene pairs that are (as a combination) specific to a single pathway. In relying on such pathway gene-pair signatures (pathway GPS), SIGORA inherently uses the status of other genes in the experimental context to identify the most relevant pathways. The current version allows for pathway analysis of human and mouse datasets. In addition, it contains pre-computed pathway-GPS data for pathways in the KEGG and Reactome pathway repositories and mechanisms for extracting GPS from user-supplied repositories.

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genesetenrichmentgosoftwarepathwayskegg

5.22 score 1 stars 1 dependents 37 scripts 351 downloads

prozor - Minimal Protein Set Explaining Peptide Spectrum Matches

Determine minimal protein set explaining peptide spectrum matches. Utility functions for creating fasta amino acid databases with decoys and contaminants. Peptide false discovery rate estimation for target decoy search results on psm, precursor, peptide and protein level. Computing dynamic swath window sizes based on MS1 or MS2 signal distributions.

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softwaremassspectrometryproteomicsexperimenthubsoftware

4.69 score 5 stars 97 scripts 417 downloads

saintexpress - Pure R Implementation of SAINTexpress

A pure R implementation of the SAINTexpress scoring engines for affinity purification-mass spectrometry data, covering both the spectral-count and intensity models, together with validation of SAINT input tables. The output mirrors the native SAINTexpress 'list.txt' format, so protein-protein interactions can be scored without external binaries. The underlying method is described in Teo et al. (2014) <doi:10.1016/j.jprot.2013.10.023>.

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massspectrometryproteomicssoftware

3.40 score 2 scripts

apbCatalogR - Look Up APB Result Fields by Meaning

Looks up the fields of AnnData Proteomics Bridge (APB) results by meaning, such as a PEP or an unnormalized intensity, without naming vendor columns. Reimplements the apb-catalog API on the bundle apb-catalog releases: reviewed catalogues, apb2's rule levels and expected answers. Reads APB results, as h5ad, Parquet or DuckDB, into anndataR objects.

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proteomicsmassspectrometrydataimportinfrastructure

3.00 score