ProteinBatcher - An end-to-end proteomics workflow with condition-aware imputation, flexible statistical modelling and interactive visualization
ProteinBatcher provides utilities to read, validate, and harmonize quantitative proteomics result tables generated by DIA-NN from data-independent acquisition mass spectrometry experiments. The package enables batch processing of multiple DIA-NN output files, consistent handling of protein identifiers and associated metadata, and transformation of tabular data into analysis-ready formats. It facilitates downstream differential abundance analysis using linear modeling frameworks based on limma, with explicit support for multivariable experimental designs including batch effects and other confounding covariates, as well as correlation-aware designs via duplicateCorrelation.
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proteomicsmassspectrometrydataimportdatarepresentationsoftwarebatcheffect
4.65 score 4 scripts 141 downloadssingIST - comparative single-cell transcriptomics between disease models and a human condition
Provides with toolkits to implement a full singIST analysis with pseudobulked Seurat objects of disease models and human data.
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singlecellclassificationtranscriptomics
4.40 score 9 scripts 184 downloads