HolobiomicsLab

Use when after running DESeq() on a DESeqDataSet and obtaining initial results via results(), use this skill when you need to (1) extract base results tables for specific…

Use when you have raw mzML files from an FTICR-MS or other direct-injection MS instrument and need to identify discrete chromatographic peaks across the m/z and retention-time…

Use when after identifying statistically significant features within individual LC-MS assays (e.g., via MB-VIP and permutation testing), use this skill when you have multiple…

Use when after discovering Mass2Motifs via LDA on preprocessed MS/MS spectra, use this skill to assign putative substructure annotations by matching each motif's fragmentation…

Use when you have an ArchR project with clustered single-cell ATAC-seq cells and want to reconstruct developmental or cellular transition trajectories.

Use when you have developed or adapted an analytical method (e.g., NPFimg for GC–MS marker identification) and need to demonstrate its reliability or improved performance over a…

Use when when processing imzML/ibd Imaging Mass Spectrometry datasets and you need to extract ion density maps for specific analytes or isotopes.

Use when when you have an observed m/z value from mass spectrometry imaging and need to annotate it with a ranked list of candidate chemical formulae.

Use when use this skill after performing Tn5 bias correction and footprint scoring on ATAC-seq BAM files when you need to inspect the spatial distribution of Tn5 insertions around…

Use when you have computed a sparse pairwise distance matrix from nearest neighbor indexes and need to group spectra into clusters.

Use when you need to containerize a C# application (e.g., AirdPro) that targets .NET Framework 4.8 and must run on Linux hosts via Docker, but the application was originally built…

Use when you have obtained a Rust source repository (e.g., mzpeak_prototyping) and need to compile it into a working command-line converter tool or library.

Use when you have raw LCMS data in mzML format and a feature table (CSV) from a peak detection pipeline (e.g., MZmine) and need to prepare these inputs for NeatMS preprocessing,…

Use when after fitting a Gaussian Process regression model to prior LC-MS gradient evaluations (where gradients are encoded as input and separation efficiency is output) — from…

Use when after fitting and optimizing a MB-PLS model on training data, apply this skill to the held-out test set (typically 10% of the original sample) to obtain unbiased…

Use when after applying two or more LC-MS alignment algorithms (such as XCMS and ncGTW) to the same dataset, use this skill to determine which produces warping functions.

Use when when you have MS/MS spectra from GNPS or other libraries and need to apply a pre-trained FIDDLE model (TCN formula predictor or Siamese rescore architecture) without…

Use when after generating ChIP pileup and local lambda (background) BEDGRAPH tracks with matched sequencing depth, use this skill to assign statistical significance scores to each…