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Name Description Author Category Runtime Version Actions
DIA-NN to CurtainPTM Converter Convert DIA-NN PTM differential analysis output to CurtainPTM upload format. Processes modified seq… CauldronGO Team utilities python 1.0.0 View
Export ASAP Exports ASAP files from an SDRF file. utilities python 1.0.0 View
Triqler Protein Quantification Protein quantification with integrated error propagation using Triqler. Propagates uncertainty from… CauldronGO Team statistics python 1.0.3 View
Lyso-IP Gating & Ranking Classifies proteins as Positive/Negative/Nonsignificant on hard significance gates, then z-score co… CauldronGO Team lysoip-qc python 1.0.0 View
Estimation Plot Generate estimation plots with effect sizes using DABEST CauldronGO Team visualization python 1.0.0 View
Protein Coverage Map Generate protein coverage maps from peptide data with intensity values CauldronGO Team utilities python 1.0.0 View
Proteomic Ruler Estimate protein copy numbers and concentrations from deep profile mass spectrometry experiments us… CauldronGO Team analysis python 0.1.0 View
Venn Diagram Generate Venn diagrams for set comparison CauldronGO Team visualization r 1.0.0 View
PhosR MaxQuant TMT Analysis Comprehensive phosphoproteomic data analysis including normalization, differential analysis, kinase… CauldronGO Team statistics r 1.0.0 View
MSFragger to CurtainPTM Converter Convert MSFragger PTM single site output to CurtainPTM upload format. Extracts PTM positions from i… CauldronGO Team utilities python 1.0.0 View
Spectronaut to CurtainPTM Converter Convert Spectronaut PTM output to CurtainPTM upload format. Supports multiple processing modes for … CauldronGO Team utilities python 1.0.0 View
Lyso-IP Organelle Coverage Two one-sided Fisher's exact tests asking whether marker genes clear the Positive/Negative gate mor… CauldronGO Team lysoip-qc python 1.0.0 View
ANCOVA Analysis Analysis of Covariance (ANCOVA) for comparing group means while controlling for covariates, with FD… CauldronGO Team analysis python 1.0.0 View
PTM Position Remapping Remap PTM positions from peptides to protein sequences using UniProt data CauldronGO Team utilities python 1.0.0 View
Data Normalization Normalize data using various scaling methods CauldronGO Team preprocessing python 1.0.0 View
Batch Effect Correction Correct for batch effects in proteomics data CauldronGO Team preprocessing r 1.0.0 View
Limma Differential Expression Linear models for differential expression analysis using limma CauldronGO Team analysis r 1.0.0 View
DNA/RNA Frame Translation Translates DNA/RNA sequences to amino acid sequences using 3-frame or 6-frame translation. Supports… Toan Phung proteomics python 1.0.0 View
Coefficient of Variation Plot Generate coefficient of variation (CV) plots for DIA-NN data quality assessment CauldronGO Team visualization python 1.0.0 View
Dose-Response Analysis Fit dose-response curves and calculate IC50 values for compound screening data CauldronGO Team analysis python 1.0.1 View
Correlation Matrix Generate correlation matrices with customizable visualization options CauldronGO Team visualization r 1.0.0 View
Lyso-IP Differential Expression Log2 fold-change and significance (limma or msqrob2, auto-selected) plus a ROAST-based whole-run ex… CauldronGO Team lysoip-qc r 1.0.0 View
Bubble Plot Heat Map Create interactive bubble plot heat maps where bubble size and color represent intensity values acr… CauldronGO Team (based on noatgnu/bubble-plot) visualization python 1.0.0 View
Lyso-IP Organelle Specificity Rewards a curated marker protein enriched toward IP, penalizes it more heavily if enriched toward W… CauldronGO Team lysoip-qc python 1.0.0 View
Fold Change Violin Plot Generate violin plots for fold enrichment analysis across organelles CauldronGO Team visualization python 1.0.0 View
PCA Analysis Principal Component Analysis for dimensionality reduction and visualization CauldronGO Team analysis python 1.0.0 View
ConSurf Conservation Analysis Protein sequence conservation analysis using ConSurf standalone. Identifies conserved and variable … Toan Phung analysis docker 1.0.0 View
MaxLFQ Normalization Label-free quantification using MaxLFQ algorithm for protein-level quantification from peptide inte… CauldronGO Team preprocessing r 1.0.0 View
Total Proteomics QC & Normalisation QC filtering and PRONE normalisation method comparison for DIA-NN total proteomics data CauldronGO Team preprocessing r 1.0.0 View
Lyso-IP Reproducibility Per-protein replicate consistency score within the IP and WCL groups for lyso-IP data CauldronGO Team lysoip-qc python 1.0.0 View
Proteomics MultiQC Report Generate comprehensive quality control reports for mass spectrometry proteomics data using pmultiqc… CauldronGO Team utilities python 1.0.0 View
Lyso-IP GO Evidence goatools enrichment test for the expected subcellular-compartment GO term(s), default lysosomal. Do… CauldronGO Team lysoip-qc python 1.0.0 View
Lyso-IP Ingestion Converts a Spectronaut, FragPipe, DIA-NN, or generic tidy search-engine export into the tidy long-f… CauldronGO Team lysoip-qc python 1.0.0 View
Peptide Library Check Check if peptides from experimental data are present in a FASTA library by generating tryptic pepti… CauldronGO Team utilities python 1.0.0 View
Total Proteomics Differential Expression Group-wise or Perseus-default imputation and limma differential expression for normalised total pro… CauldronGO Team analysis r 1.0.0 View
PHATE Analysis PHATE (Potential of Heat-diffusion for Affinity-based Trajectory Embedding) for dimensionality redu… CauldronGO Team analysis python 1.0.0 View
Missing Value Imputation Impute missing values using various methods CauldronGO Team preprocessing python 1.0.0 View