Claude Skills by HolobiomicsLab

Use when after applying BPCA imputation to a filtered metabolite matrix

Use when you have acquired raw mass spectrometry imaging data in imzML

Use when you have acquired imaging mass spectrometry (IMS) data stored

Use when when you have one or more imzML files containing mass spectrometry

Use when you have received paired .imzML (XML metadata) and .ibd (binary

Use when when deploying a high-throughput molecular classification API

Use when you are repeatedly querying or iterating over multidimensional

Use when after feature filtering and clustering have been completed in

Use when when you have experimental UHPLC-HRMS/MS or direct infusion

Use when you have a collection of compound structures in SDF format (e.g.,

Use when you have candidate metabolite structures (from database lookup

Use when you have experimental peak lists (m/z, retention time, intensity)

Use when when you have a list of SMILES strings representing chemical

Use when when processing collections of in-silico mass spectra from OMSLs

Use when you have aligned, imputed time-resolved mass spectrometric data

Use when you have an LCMS feature table (from XCMS, MS-DIAL, MZmine2,

Use when you have clustered peak networks from INADEQUATE NMR spectra

Use when you have raw INADEQUATE NMR spectrum files (e.g., in standard

Use when you have a GNPS DBResult file from spectral library matching

Use when gNPS has stopped supplying ClassyFire ontology information for

Use when you have an annotated MS/MS spectral dataset with structure

Use when when you have raw MS/MS spectra from repositories like GNPS

Use when you have a ranked list of library candidates (top 2000 by MS2Deepscore)

Use when you have candidate library matches from MS2Deepscore ranking

Use when you have compressed mzML.gz files and need to retrieve specific

Use when when running Mass2SMILES inference on a TensorFlow-CPU build

Use when you have trained two or more graph neural network models on

Use when when training embeddings from MS/MS spectra data where you need

Use when when you have a dataset of molecules with experimentally measured

Use when designing multi-batch LC/GC-MS experiments where you need to

Use when when configuring a multi-well plate design (96-well, 384-well,

Use when you have a Sciex Multiquant TXT export file containing a metabolomics

Use when apply IOKR when you have BGCs with structural predictions based

Use when a web application receives mass spectrometry data through heterogeneous

Use when before attempting to run QCxMS2 for the first time, after updating

Use when when setting up matchms for the first time in a new environment,

Use when after installing a package via conda or pip from a distribution

Use when when deploying a new Python package in a reproducible analysis

Use when after cloning the ENPKG repository and installing dependencies

Use when you have DIA raw mass spectrometry files from multiple instrument

Use when when preprocessing a heterogeneous spectral library (e.g., GNPS

Use when when you have raw or semi-processed mass spectrometry data files

Use when when adopting a mass spectrometry data processing tool (e.g.,

Use when you have a large, mixed-instrument GNPS spectral dataset and

Use when you have a time-series of repeated QCpool (pooled quality control)

Use when you have raw LA-ICP-MS image data (line-by-line, spot-wise,

Use when when you have obtained a raw Orbitrap mass spectrometry file

Use when when you have implemented or modified a data ingestion module

Use when you have a preprocessed peak table with statistically significant

Use when when visualizing 2D peak maps (x=m/z, y=retention time or ion