rformassspectrometry / Spectra

Low level infrastructure to handle MS spectra

https://rformassspectrometry.github.io/Spectra/

rformassspectrometry/Spectra Issues

Interpretation of matchSpectra() and plotting results of plotSpectraMirror()
Updated 2 months ago
Coerce Spectra to DataFrame
Closed 2 months ago3
adduct type
Updated 4 months ago1
MS-imaging support / MsBackendImzML
Updated 4 months ago3
Add possibility to change the file path for a `MsBackendMzR`
Closed 4 months ago2
Suggesion for combinePeaksData
Closed 4 months ago4
Visualize, use plotSpectraMirror function to draw spectrum matching results
Closed 4 months ago1
Adjust precursor m/z values for MS2 spectra from Waters instruments
Closed 6 months ago5
Fix is.vector()
Updated 6 months ago3
Smoothing along the time domain (chromatographic peaks)
Closed 6 months ago1
AnnotationFilter-based filtering of Spectra objects?
Closed 7 months ago3
Add a method to calculate the entropy of all spectra
Closed 7 months ago1
Problem with MGF import - object: mz values have to be sorted increasingly
Closed 7 months ago3
Problem with Waters raw file
Updated 7 months ago2
Memory issues and (potential) chunk-wise processing of peaks data
Closed 10 months ago8
Ensure all methods working on peaksData use the chunk-wise processing
Updated 10 months ago
`bin` function *create* peaks of intensity 0
Closed 10 months ago4
`filterFourierTransformArtefacts` fails when used with other processings
Closed a year ago4
Add a filterPrecursorPeaks function
Closed a year ago5
Add documentation on MS entropy-based similarity calculation
Closed a year ago4
Add a filterUniquePrecursorMz method
Closed a year ago4
Add a filterPrecursorIsotopes method
Closed a year ago4
Import mspLib format
Closed a year ago4
Add scalePeaks function
Closed a year ago
Add fusePeaks function
Closed a year ago8
New feature: group and summarised Spectra
Updated a year ago2
API CHANGE: support peaksData to return data.frame or matrix
Updated a year ago11
Add validator method to MsBackend checking for ordered m/z values
Closed a year ago2
Add support for peak annotations
Closed a year ago
Split Spectra documentation into smaller chunks
Updated a year ago
Add a reduce method
Closed a year ago4
Add a deisotope function
Closed a year ago
Version 1.8.x Spectra objects not readable by earlier package versions?
Closed a year ago2
filterMzValues
Closed 2 years ago10
"chunkyfied" processing
Closed 2 years ago2
A tutorial and specification for building backends
Closed 2 years ago16
Check if a backend supports parallel processing
Closed 2 years ago7
MzBackendMzR misleading error with empty file list and misleading behavior with `files` argument
Closed 2 years ago3
`setBackend` to `MsBackendMemory` fails for empty `Spectra`
Closed 2 years ago2
Re-evaluate automatic detection of peaks variables
Closed 2 years ago1
Function to find/visualise contaminants
Updated 2 years ago2
pickPeaks fails to centroid if no flanking zeroes are present
Updated 2 years ago4
Externalize hdf5 backend?
Closed 2 years ago3
Bug in containsMz()
Closed 2 years ago7
filterPrecursorMzRange
Updated 2 years ago2
An attempt to convert a spectra file to a data frame
Closed 2 years ago7
To extract method info from mzXML file(s)?
Closed 2 years ago1
compareSpectra inconsistency?
Closed 2 years ago4
A more efficient in-memory backend
Closed 2 years ago3
Discussion: spectraData,spectraData<- to support also data.frame or other two-dimensional data structues
Updated 2 years ago