Use when when you have a query electron ionization mass spectrum (m/z and intensity pairs) and need to identify the most similar spectra from an MSP-formatted spectral library.
Use when after normalizing an MSI pixel array to TIC or an internal standard, when the raw pixel intensity distribution spans multiple orders of magnitude and produces images with…
Use when processing raw IM-MS data (Agilent MassHunter .d or UIMF format) that exhibits isolated high-intensity noise artifacts or instrumental artifacts that appear as discrete,…
Use when when you have raw or unnormalized gene expression data from microarray experiments (e.
Use when when you have a multi-step computational chemistry or molecular modeling pipeline (3+ sequential or parallel stages) that must process many molecules, each requiring…
Use when after extracting and grouping fragments from top x% TIC-filtered replicate spectra for a given feature, to quantify which fragments consistently appear across replicates.
Use when when you have an unknown compound's mass spectrum (m/z peaks and intensities in .mgf or equivalent format) and need to identify structurally related metabolites — from…
Use when you have two peak-picked, conventionally aligned LC-MS metabolomics datasets (e.
Use when when you have raw MS/MS mass spectrometry data and need to submit it to the Mass2SMILES Docker inference container for structure and functional group prediction.
Use when when working with feature abundance tables (rows=features, columns=samples)
Use when you have xcms-processed LC-MS data with detected misaligned feature groups and need to recover the underlying raw retention time–intensity profiles for each feature and…
Use when after running XCMS-based alignment on LC-MS datasets with hundreds of samples or data acquisition periods longer than a week, when the assumption that all m/z bins in the…
Use when you need to verify that a GitHub Actions workflow (such as a Build and Publish pipeline) executes successfully on a specific branch (e.g., release branch) and produces a…
Use when you have computed raw strain correlation scores (based on shared strain membership) between genomic and metabolomic objects of heterogeneous sizes, and you need to…
Use when when you have raw mass spectrometry imaging data tensors and need to build a trainable deep-learning classifier that outputs class probabilities (tumor vs.
Use when you need to verify that a QIIME 2 artifact (e.g., a Chemical Feature Tree from q2-qemistree, a FeatureTable[Frequency], or a Phylogeny[Rooted] object) has been correctly…
Use when you have raw or peak-picked mass spectrometry data in HDF5 format that needs to be loaded into memory for downstream processing (feature alignment, isotope detection, CCS…
Use when you have experimental fragment m/z peaklists from Q-Exactive orbitrap, Agilent Q-TOF, Bruker Q-TOF, or SCIEX Q-TOF UHPLC-HRMS/MS instruments (in CSV or mzML-derived table…
Use when you have .msp spectral library files with compound names but lack standardized chemical identifiers (SMILES, InChI, InChI Key, CAS number, IUPAC names, or molecular…
Use when after noise filtering and baseline correction have been applied to mass spectrometry data (DI-MS, ASAP-MS, LDI-MS, or other high-throughput MS formats in mzML, mzXML, or…
Use when you have a preprocessed unknown sample spectrum (m/z peaks and intensities) from high-throughput mass spectrometry (DI-MS, ASAP-MS, or ambient ionization methods — from…
Use when when you have millions of high-dimensional objects (e.g., MS/MS spectra converted to feature-hashed vectors) and need to compute pairwise similarities or retrieve nearest…
Use when you have a new fragmentation acquisition strategy (e.g., a weighted exclusion variant, alternative TopN ranking, or dynamic isolation window rule) that you wish to…
Use when after implementing or modifying Python library functions (such as utility functions in cooltools.lib subpackages) to verify correctness and identify gaps in test coverage…
Use when analyzing RNA-seq count data from a DESeq2 workflow where you have fitted negative binomial generalized linear models and need to extract final results.
Use when preparing labeled LC-MS peak data for neural network training and you need to decide whether class imbalance in your dataset should be preserved or corrected in batch…
Use when when you have preprocessed MALDI-MSI data (in msimat format) and want to determine whether abundant peaks are actually molecular adducts of simpler parent ions rather…
Use when you have PSI (percent-spliced-in) matrices calculated independently for two or more biological conditions, each with two or more replicate samples, and you want to…
Use when after completing metabolite annotation of LC-MS AIF features using the annotateRC function, when you need to persist ranked candidate matches, inspect multiple candidate…
Use when when you have leiden or louvain cluster assignments in single-cell data (stored in adata.obs) and need to identify cluster-specific marker genes.
Use when your metabolomics dataset contains missing values below a known detection limit (left-censored MNAR data), and you need to recover these values while respecting the…
Use when when comparing two or more MSMS spectra using intensity-weighted similarity measures (cosine similarity, modified cosine, or neutral loss similarity), and the spectra…
Use when raw MS quantification data (feature-by-sample intensity matrix) shows systematic variation in detector response across the run sequence—i.e., when the same analyte…
Use when you have a combined EI mass spectral library (MSP format) lacking experimental RI values, access to NIST ri.dat and USER.
Use when you have peak-picked LC-MS metabolomics data in a tabular format (R data frame) with columns for mass-to-charge ratio, retention time, feature identifiers, adduct…
Use when you have uploaded MS/MS data to MassIVE with validated sample-information
Use when you have high-resolution MS2 data in .ms2 format from lipid A samples and need to perform automated structure annotation to identify lipid A molecular variants and their…
Use when after fitting a Multi-Block PLS (MB-PLS) discriminant or regression model on multi-assay LC-MS intensity data (e.g., HPOS, LPOS, LNEG blocks), and you need to identify…
Use when you have extracted tabular data (e.g., protocol descriptions, sample preparation steps) into an intermediate JSON representation and need to subset records by type or…
Use when when you have per-feature quality metrics (such as CV values from NMR or MS reproducibility analysis) and need to: (1) confirm that a specified proportion of features…
Use when you have computed a histogram of pairwise mass differences from MS imaging data and need to (1) identify which observed mass differences correspond to biologically…
Use when after LDA inference has produced a trained motifset (motifset.json or motifset_optimized.json) with Mass2Motif probability distributions over fragments and neutral losses.
Use when after running salmon quant with the --writeMappings/-z flag to produce SAM output, or when investigating discrepancies between the number of mapped reads reported in…
Use when you have extracted raw tabular metadata into JSON form using the MESSES extract command and need to confirm the extraction is accurate before conversion to a…
Use when after marker identification or metabolite annotation has produced a curated list of compound IDs (e.g., KEGG IDs or CAS numbers) and you need to determine which metabolic…
Use when when you need to quantify and compare the filtering efficacy of mutually exclusive noise-threshold methods on the same input mass spectrum, or when validating that a…
Use when when raw spectral data exists in one mass spectrometry file format but downstream analysis requires a different format; when integrating spectra from multiple sources or…
Use when after installing R or modifying an R environment via conda, package managers, or container images; before running any pipeline step that depends on R packages for…
Use when preparing ion image data for representation learning in mass spectrometry imaging, specifically when you need to augment raw ion images to generate pairs of diverse views…
Use when you have extracted retention times at peak maxima (rtFittedAPEX) from extracted-ion chromatograms (XICs) of known internal RT calibrants (e.
Use when you have a precomputed expected contact frequency table (TSV with columns: dist_bp, contact_frequency, n_valid) derived from cooler Hi-C matrices and need to generate a…
Use when when you need to prototype, test, or benchmark MS1-only acquisition strategies on a defined set of metabolites (e.
Use when you have replicate MS/MS spectra with labeled fragment recurrence frequencies and need to select an optimal frequency threshold (beyond the default 0.1) that maximizes…
Use when when you need to reverse-engineer or formally document the computational steps within a closed or under-documented scientific software module—particularly when the…
Use when when you have processed Cardinal MSI data (normalized peak intensities,
Use when when processing untargeted LC-MS data with SLAW and observing incomplete feature detection across the sample cohort—i.e., features present in some samples but with…
Use when you have a trained GNN model (stored as .h5 weights) and molecular graph representations (SMILES strings and/or 3D coordinates), and you need to compute predicted CCS…
Use when when setting up a DESeqDataSet from count matrices or transcript quantification, you must specify a design formula before running DESeq() if your experiment has batch…
Use when adding a new converter class to MSMetaEnhancer or when modifying an existing converter's __init__ method to add/remove conversions.
Use when you have an unknown compound's mass spectrum (m/z peaks and intensities) in . — from HolobiomicsLab/asb-skill-collections