Use when when you have computed per-bin insulation scores from a Hi-C cooler file using cooltools.insulation and need to identify discrete genomic boundaries that separate…
Use when after calculating differential methylation across samples using calculateDiffMeth(), when you need to separately enumerate and extract hyper-methylated (increased…
Use when when Rapid QC-MS receives vendor-format LC-MS acquisition files from instrument data folders and must prepare them for automated QC checks and MS-DIAL processing.
Use when when you need to extract both local spatial patterns and global long-range dependencies from sequential or spectral data (e.g., 1H NMR spectra), and neither CNNs nor…
Use when you have paired-end or single-end RNA-seq reads (FASTQ format) and a reference transcriptome (FASTA), and you need to estimate transcript-level abundances (NumReads and…
Use when after training a transformer-encoder-based mass spectrometry embedding model (e.
Use when when your DDA-mode LC-MS/MS data exhibits chimeric spectra patterns that differ systematically from the reference training set used in DNMS2Purifier, or when you wish to…
Use when you have high-throughput replicate measurements (e.g., mass spectrometry metabolomics) on biological replicates and need to identify which sample pairs exhibit…
Use when when you have deconvolved GC-MS spectra (post-deconvolution output compatible with GNPS_GC input specification) and need to group them by chemical similarity to construct…
Use when when you have discovered Mass2Motifs from MS2LDA topic modeling and need to automatically annotate them by finding the most structurally similar known spectra in a…
Use when you have a feature table from LC-MS data alongside blank (solvent-only) sample runs, and you want to remove features whose intensity in study samples is not substantially…
Use when after inferring Mass2Motif definitions from LDA modeling when you need to build a network representation of motif relationships.
Use when you have tabular metabolomics data (tab-delimited or Sciex OS format) and need to apply a specialized R package's analysis pipeline—such as mzQuality—that requires…
Use when you have preprocessed mass spectrometry data (peak-picked, baseline-corrected)
Use when when constructing a sample list from an Excel template for LC/GC-MS analysis, you must classify each QC sample by type before proceeding to plate layout and randomization…
Use when you need to create a synthetic chemical population for testing data-dependent acquisition (DDA) strategies in a simulation environment before committing to real mass…
Use when when comparing two or more MSMS spectra and you need to emphasize structural relationships revealed by neutral losses (mass differences between precursor and fragment…
Use when when you have an unknown MSMS spectrum (precursor m/z and fragment ions) and need to discover structurally related compounds from a spectral library.
Use when after fitting a linear model with lmFit on voom-transformed or log2-normalized RNA-seq or microarray expression matrices, apply eBayes moderation to moderate gene-wise…
Use when when converting raw metabolomics data (tab-delimited text files, Sciex OS exports) into a structured object for batch processing, or when you need to organize…
Use when reading mass spectral library files (particularly MoNA EI or MS2 libraries) where structural metadata like SMILES information is embedded in general-purpose fields (e.g.,…
Use when you have MSI intensity data exported from MSiReader, SCiLS, or Cardinal as plain-text CSV files or as Cardinal MSProcessedImagingExperiment/MSContinuousImagingExperiment…
Use when you have an MS/MS spectrum and a ProForma 2.0 peptidoform specification,
Use when you observe discrepancies in mapping rate or per-transcript quantification between two salmon implementations, or when the default chain-pruning thresholds…
Use when designing multi-batch LC/GC-MS experiments where samples belong to multiple groups or conditions and you need to ensure that each injection plate receives a balanced…
Use when after performing assignment operations (assign_ri, assign_smiles) or combining multiple library objects (e.
Use when you have an unknown mass spectrum (or a representative metabolite spectrum from public data) and need to identify it by comparing it against a large reference…
Use when you have modified the Scanpy codebase (e.g., added a feature or bugfix) and need to confirm that all unit and integration tests pass before submitting a pull request, or…
Use when when you have fitted one or more regression models (linear or polynomial) to external calibration standards in MS data and need to verify model adequacy before applying…
Use when when you have a Python package repository on GitHub and need to automatically verify that pull requests and commits pass unit tests and meet code quality standards before…
Use when when you have raw or processed direct-infusion MS (DI-MS) or ASAP-MS spectra as mz/intensity pairs and need to rapidly identify salient peaks for species authentication,…
Use when after generating a count matrix from fragment data using pp.add_tile_matrix, pp.make_peak_matrix, or pp.make_gene_matrix in SnapATAC2.
Use when you have peak intensity vectors from LC/GC-MS experiments with corresponding QC (quality control) sample measurements, and you need to correct for batch…
Use when when you need to validate that a package's periodic integration test suite (distinct from unit tests) passes as expected, or when you must collect and communicate…
Use when you have LC-MS/MS spectra (MGF, mzXML, mzML, or mzData format) and either raw genome nucleotide sequences or antiSMASH/BOA genome mining tool output, and you need to…
Use when when you need to empirically validate that one mass spectrometry data processing library achieves higher throughput than competing alternatives.
Use when when comparing GNPS chemical annotations across two or more groups of samples (defined by ReDU sample-information categories such as sample type, extraction method, or…
Use when you have aligned single-cell ATAC-seq data as BAM files or fragment files (TSV format with genomic coordinates) and need to prepare it for spectral embedding, clustering,…
Use when you need to verify whether a GitHub Actions workflow badge (e.g., main.yml) accurately reports the CI pipeline's true pass/fail status.
Use when you have centroid mzML files from LC-MS experiments (converted from Thermo .raw or other vendor formats) and need to identify and quantify individual chemical features…
Use when when processing LC-MS peak tables from isotope tracing experiments where multiple ionization adducts ([M+H]+, [M+Na]+, [M+NH4]+, etc.) and in-source fragments have…
Use when you have completed batch spectral searches against multiple domain-specific MASST tools (via Fast Search API or individual domain searches) and need to combine and…
Use when after running annotateRC to generate ranked candidate annotations for LC-MS AIF features, when you need to confirm that (1) the top-ranked candidate match is chemically…
Use when after executing a Nextflow-based MS-DIAL workflow on .mzML LC-HRMS metabolomics data using Docker or Singularity container backends.
Use when you have a normalized single-cell expression matrix (e.g., after SCTransform) and need to compute gene-level covariance structure for pathway enrichment analysis (e.g.,…
Use when after selecting statistically significant features from multi-assay LC-MS metabolomics datasets (e.g., via MB-VIP and permutation testing with p < 0.01).
Use when when you need to verify whether a specific mass spectrometry instrument platform (vendor and model), acquisition mode (e.g., targeted, ddMS2-topN, AIF, direct infusion,…
Use when your MetaboSet object contains missing values (marked as NA) in the expression matrix after quality flagging, but you need complete data for multivariate analysis.
Use when you have a tandem mass spectrum (MsmsSpectrum) from a known peptide and need to determine what fraction of observed peaks can be explained by expected fragment ions.
Use when when rendering a treemap of qc_summary() output showing ion counts and percentages by filter status (passed/failed), and you need a perceptually uniform,…
Use when you have a tandem mass spectrum (MSMS) loaded via USI and wish to maximize the interpretability of observed peaks.
Use when you are preparing to run Hi-C data normalization or read alignment filtering steps that depend on Python modules (iced, pysam, numpy, scipy) and you need to ensure…
Use when when you have an Excel file uploaded by a user following the InjectionDesign template schema and need to convert it into a modifiable, structured sample list that…
Use when you have ATAC-seq BAM alignments with classified motif sites (bound vs. unbound based on chromatin accessibility or binding thresholds) and wish to detect and visualize…
Use when when extending a multi-service project (like MAGMa with its four subproject components) to container orchestration, and you need to ensure each microservice (magmaweb,…
Use when when you have LC-MS/MS acquisitions in DDA mode and need to train a customized DNMS2Purifier model to purify chimeric MS/MS spectra specific to your experimental…
Use when you need to verify that a GitHub Actions workflow (such as a development build release pipeline) has completed successfully, capture its build artifacts (installers,…
Use when you have cloned a scientific Python project (e.g., scverse/scanpy) and need to verify that your local development environment matches the CI specification before…
Use when after training a GNN-RT model on preprocessed molecular graph data (from Train.py) or after applying transfer learning to an in-house dataset (from Transferlearning.
Use when when you have extracted retention times from the top detected MS1 features in a LC-MS run and need to evaluate whether the gradient spreads those compounds efficiently…